diff --git a/frontend/src/lib/components/graph/FlowGraphV2.svelte b/frontend/src/lib/components/graph/FlowGraphV2.svelte
index 052df58d63..08cd4e80ca 100644
--- a/frontend/src/lib/components/graph/FlowGraphV2.svelte
+++ b/frontend/src/lib/components/graph/FlowGraphV2.svelte
@@ -13,7 +13,8 @@
 		Controls,
 		ControlButton,
 		SvelteFlowProvider,
-		type Viewport
+		type Viewport,
+		SelectionMode
 	} from '@xyflow/svelte'
 	import {
 		graphBuilder,
@@ -388,10 +389,11 @@
 		insert: (detail) => {
 			onInsert?.(detail)
 		},
-		select: (modId) => {
+		select: (mod: string | FlowModule) => {
 			if (!notSelectable) {
 				// TODO: Handle Ctrl/Cmd and Shift modifiers when node-level click events are available
 				// For now, normal click behavior
+				const modId = typeof mod === 'string' ? mod : mod.id
 				selectionManager.selectId(modId)
 				onSelect?.(modId)
 			}
@@ -423,7 +425,7 @@
 			delete expandedSubflows[id]
 			expandedSubflows = expandedSubflows
 		},
-		updateMock: (detail) => {
+		updateMock: (detail: any) => {
 			onUpdateMock?.(detail)
 		},
 		testUpTo: (id: string) => {
@@ -472,8 +474,8 @@
 		selectionManager.handleKeyDown(event, nodes)
 	}
 
-	function handleKeyUp(event: KeyboardEvent) {
-		selectionManager.handleKeyUp(event)
+	function handleKeyUp(_event: KeyboardEvent) {
+		// Keep for potential future use
 	}
 
 	async function updateStores() {
@@ -767,8 +769,12 @@
 				connectionLineType={ConnectionLineType.SmoothStep}
 				defaultEdgeOptions={{ type: 'smoothstep' }}
 				preventScrolling={scroll}
+				selectionOnDrag={selectionManager.mode === 'rect-select'}
+				elementsSelectable={true}
+				selectionMode={SelectionMode.Partial}
+				selectionKey={selectionManager.mode === 'rect-select' ? null : 'Shift'}
+				panActivationKey={selectionManager.mode === 'rect-select' ? 'Shift' : null}
 				zoomOnDoubleClick={false}
-				elementsSelectable={false}
 				elevateNodesOnSelect={false}
 				{proOptions}
 				nodesDraggable={false}
@@ -791,15 +797,11 @@
 							selectedNodes={nodes.filter((node) => selectionManager.selectedIds.includes(node.id))}
 						/>
 					</NodeContextMenu>
-
-					<SelectionTool
-						selectionMode={selectionManager.mode}
-						onNodesSelected={(nodeIds, addToExisting) =>
-							selectionManager.selectNodes(nodeIds, addToExisting, modules, nodes)}
-						{nodes}
-					/>
 				{/if}
 
+				<!-- SelectionTool for handling selection changes and filtering -->
+				<SelectionTool {nodes} {modules} {selectionManager} />
+
 				{#if leftHeader}
 					<div class="absolute top-2 left-2 z-10">
 						{@render leftHeader()}
@@ -882,4 +884,8 @@
 	:global(.svelte-flow__edgelabel-renderer) {
 		@apply z-50;
 	}
+
+	:global(.svelte-flow__selection) {
+		display: none;
+	}
 </style>
diff --git a/frontend/src/lib/components/graph/SelectionTool.svelte b/frontend/src/lib/components/graph/SelectionTool.svelte
index 143baea07f..b69e995aef 100644
--- a/frontend/src/lib/components/graph/SelectionTool.svelte
+++ b/frontend/src/lib/components/graph/SelectionTool.svelte
@@ -1,208 +1,61 @@
 <script lang="ts">
-	import { useSvelteFlow, type XYPosition } from '@xyflow/svelte'
-	import { NODE } from './util'
+	import { useOnSelectionChange, useStore, type Node } from '@xyflow/svelte'
 
 	interface Props {
-		selectionMode: 'normal' | 'rect-select'
-		onNodesSelected: (nodeIds: string[], addToExisting: boolean) => void
 		nodes: any[]
+		modules?: any[]
+		selectionManager: any
 	}
 
-	let { selectionMode, onNodesSelected, nodes }: Props = $props()
+	let { nodes, modules, selectionManager }: Props = $props()
 
-	const { screenToFlowPosition } = useSvelteFlow()
+	// Get store to access selectionRect
+	const store = useStore()
 
-	let isDrawing = $state(false)
-	let startPosition: XYPosition | null = $state(null)
-	let endPosition: XYPosition | null = $state(null)
-	let rect: DOMRect | null = $state(null)
+	// Handle selection changes from SvelteFlow
+	useOnSelectionChange(({ nodes: selectedNodes, edges: _selectedEdges }) => {
+		console.log('dbg useOnSelectionChange', selectedNodes, _selectedEdges)
+		// Notes are already non-selectable, so no filtering needed
+		const selectedNodeIds = selectedNodes.map((node: Node) => node.id)
 
-	// Global handler to handle middle-click panning in rect mode
-	function handleGlobalPointerDown(event: PointerEvent) {
-		if (selectionMode === 'rect-select' && event.button === 1) {
-			// Find the SvelteFlow element and dispatch the event to it
-			const flowElement = document.querySelector('.svelte-flow')
-			if (flowElement) {
-				const syntheticEvent = new PointerEvent('pointerdown', {
-					bubbles: true,
-					pointerId: event.pointerId,
-					button: event.button,
-					buttons: event.buttons,
-					clientX: event.clientX,
-					clientY: event.clientY,
-					screenX: event.screenX,
-					screenY: event.screenY
-				})
-				flowElement.dispatchEvent(syntheticEvent)
-			}
+		if (selectedNodeIds.length > 0) {
+			selectionManager.selectNodes(selectedNodeIds, false, modules, nodes)
+		} else if (selectedNodes.length === 0) {
+			// Clear selection when SvelteFlow selection is cleared
+			selectionManager.clearSelection()
 		}
-	}
+	})
 
-	function onPointerDown(event: PointerEvent) {
-		if (selectionMode !== 'rect-select') return
-
-		// Allow middle-click (button 1) to pass through for graph panning
-		if (event.button === 1) {
-			// Stop the event from being handled by this overlay
-			event.stopPropagation()
-			// Re-dispatch to SvelteFlow
-			handleGlobalPointerDown(event)
-			return
+	// Compute selection box bounds
+	let selectionBoxBounds = $derived(() => {
+		const rect = store.selectionRect
+		if (!rect) {
+			return null
 		}
 
-		// Only handle left-click (button 0) for rectangle selection
-		if (event.button !== 0) return
-
-		// Capture pointer to continue tracking outside the element
-		const target = event.currentTarget as Element
-		target?.setPointerCapture?.(event.pointerId)
-
-		// Use page coordinates as reference
-		rect = target.getBoundingClientRect()
-		startPosition = {
-			x: event.pageX - rect.left,
-			y: event.pageY - rect.top
-		}
-		endPosition = startPosition
-		isDrawing = true
-		event.preventDefault()
-	}
-
-	function onPointerMove(event: PointerEvent) {
-		if (!isDrawing || !rect) return
-
-		// Use page coordinates as reference
-		endPosition = {
-			x: event.pageX - rect.left,
-			y: event.pageY - rect.top
-		}
-	}
-
-	function onPointerUp(event: PointerEvent) {
-		if (!isDrawing || !startPosition || !endPosition || !rect) return
-
-		// Only proceed if we have a meaningful selection area
-		const deltaX = Math.abs(endPosition.x - startPosition.x)
-		const deltaY = Math.abs(endPosition.y - startPosition.y)
-
-		if (deltaX > 5 || deltaY > 5) {
-			// Convert the start and end positions to absolute positions
-			const absoluteStartPosition = {
-				x: startPosition.x + rect.left,
-				y: startPosition.y + rect.top
-			}
-			const absoluteEndPosition = {
-				x: endPosition.x + rect.left,
-				y: endPosition.y + rect.top
-			}
-
-			// Convert to flow coordinates
-			const flowStart = screenToFlowPosition({
-				x: Math.min(absoluteStartPosition.x, absoluteEndPosition.x),
-				y: Math.min(absoluteStartPosition.y, absoluteEndPosition.y)
-			})
-
-			const flowEnd = screenToFlowPosition({
-				x: Math.max(absoluteStartPosition.x, absoluteEndPosition.x),
-				y: Math.max(absoluteStartPosition.y, absoluteEndPosition.y)
-			})
-
-			// Find nodes within the selection rectangle
-			const selectedNodeIds = getNodesInFlowRectangle({
-				x1: flowStart.x,
-				y1: flowStart.y,
-				x2: flowEnd.x,
-				y2: flowEnd.y
-			})
-
-			if (selectedNodeIds.length > 0) {
-				onNodesSelected(selectedNodeIds, event.shiftKey)
-			}
-		}
-
-		// Reset state
-		isDrawing = false
-		startPosition = null
-		endPosition = null
-		rect = null
-	}
-
-	function getNodesInFlowRectangle(rect: {
-		x1: number
-		y1: number
-		x2: number
-		y2: number
-	}): string[] {
-		const minX = Math.min(rect.x1, rect.x2)
-		const maxX = Math.max(rect.x1, rect.x2)
-		const minY = Math.min(rect.y1, rect.y2)
-		const maxY = Math.max(rect.y1, rect.y2)
-
-		return nodes
-			.filter((node) => {
-				// Exclude note nodes from selection (similar to "Select All" behavior)
-				if (node.type === 'note') return false
-
-				const nodeMinX = node.position.x
-				const nodeMaxX = node.position.x + NODE.width
-				const nodeMinY = node.position.y
-				const nodeMaxY = node.position.y + NODE.height
-
-				// Check if node intersects with selection rectangle
-				return !(nodeMaxX < minX || nodeMinX > maxX || nodeMaxY < minY || nodeMinY > maxY)
-			})
-			.map((node) => node.id)
-	}
-
-	const previewNote = $derived.by(() => {
-		if (!startPosition || !endPosition) return null
+		// selectionRect is already in the correct coordinate system relative to the flow container
+		// Just return it directly
 		return {
-			position: {
-				x: Math.min(startPosition.x, endPosition.x),
-				y: Math.min(startPosition.y, endPosition.y)
-			},
-			size: {
-				width: Math.abs(endPosition.x - startPosition.x),
-				height: Math.abs(endPosition.y - startPosition.y)
-			}
+			x: rect.x,
+			y: rect.y,
+			width: rect.width,
+			height: rect.height
 		}
 	})
 </script>
 
-{#if selectionMode === 'rect-select'}
+<!-- Render custom selection box during drag selection -->
+{#if selectionBoxBounds()}
+	{@const bounds = selectionBoxBounds()!}
 	<div
-		class="selection-overlay"
-		onpointerdown={onPointerDown}
-		onpointermove={onPointerMove}
-		onpointerup={onPointerUp}
-		role="button"
-		tabindex="0"
-		aria-label="Click and drag to select nodes"
+		class="absolute rounded cursor-pointer bg-surface-selected/30 border border-accent/30 pointer-events-none"
+		style="
+			left: {bounds.x}px;
+			top: {bounds.y}px;
+			width: {bounds.width}px;
+			height: {bounds.height}px;
+			z-index: 10;
+		"
 	>
-		<!-- Preview selection rectangle while drawing -->
-		{#if previewNote && isDrawing}
-			<div
-				class="absolute border border-accent/30 pointer-events-none bg-surface-selected/30"
-				style="
-					width: {previewNote.size.width}px;
-					height: {previewNote.size.height}px;
-					transform: translate({previewNote.position.x}px, {previewNote.position.y}px);
-				"
-			></div>
-		{/if}
 	</div>
 {/if}
-
-<style>
-	.selection-overlay {
-		pointer-events: auto;
-		position: absolute;
-		top: 0;
-		left: 0;
-		z-index: 5;
-		height: 100%;
-		width: 100%;
-		cursor: crosshair;
-		touch-action: none;
-	}
-</style>
diff --git a/frontend/src/lib/components/graph/noteManager.svelte.ts b/frontend/src/lib/components/graph/noteManager.svelte.ts
index f6964abe3b..fb46a44317 100644
--- a/frontend/src/lib/components/graph/noteManager.svelte.ts
+++ b/frontend/src/lib/components/graph/noteManager.svelte.ts
@@ -215,7 +215,7 @@ export class NoteManager {
 			height: size.height,
 			zIndex: zIndex ?? -2000, // Use provided zIndex or fallback
 			draggable: isGroupNote ? false : editMode && !note.locked,
-			selectable: true
+			selectable: false
 		}
 	}
 
diff --git a/frontend/src/lib/components/graph/renderers/nodes/NoteNode.svelte b/frontend/src/lib/components/graph/renderers/nodes/NoteNode.svelte
index a2dfbdaf7f..612de13f70 100644
--- a/frontend/src/lib/components/graph/renderers/nodes/NoteNode.svelte
+++ b/frontend/src/lib/components/graph/renderers/nodes/NoteNode.svelte
@@ -20,11 +20,11 @@
 			// Callback for layout calculations (needed in both edit and view modes)
 			onTextHeightChange?: (height: number) => void
 		}
-		selected?: boolean
 		dragging?: boolean
 	}
 
-	let { data, selected = false, dragging = false }: Props = $props()
+	let { data, dragging = false }: Props = $props()
+	let selected = $state(false)
 
 	// Get NoteEditor context for edit mode
 	const noteEditorContext = getNoteEditorContext()
diff --git a/frontend/src/lib/components/graph/selectionUtils.svelte.ts b/frontend/src/lib/components/graph/selectionUtils.svelte.ts
index 3b408f1385..dd5f8c1420 100644
--- a/frontend/src/lib/components/graph/selectionUtils.svelte.ts
+++ b/frontend/src/lib/components/graph/selectionUtils.svelte.ts
@@ -10,9 +10,6 @@ export interface SelectionState {
 export class SelectionManager {
 	public selectedIds = $state<string[]>([])
 	#selectionMode = $state<'normal' | 'rect-select'>('normal')
-	#modeSource = $state<'button' | 'keyboard' | 'temporary'>('button')
-	#previousMode = $state<'normal' | 'rect-select'>('normal')
-	#cmdKeyPressed = $state<boolean>(false)
 
 	constructor() {}
 
@@ -29,39 +26,10 @@ export class SelectionManager {
 	}
 
 	set mode(mode: 'normal' | 'rect-select') {
-		this.#previousMode = this.#selectionMode
 		this.#selectionMode = mode
-		// Default to button source when mode is set directly (for backward compatibility)
-		if (this.#modeSource !== 'temporary') {
-			this.#modeSource = 'button'
-		}
 		// Note: No automatic selection clearing when changing modes - preserve current selection
 	}
 
-	// Toggle mode temporarily (for cmd key hold behavior)
-	toggleModeTemporary() {
-		this.#previousMode = this.#selectionMode
-		this.#modeSource = 'temporary'
-		this.#selectionMode = this.#selectionMode === 'normal' ? 'rect-select' : 'normal'
-	}
-
-	// Toggle mode persistently (for cmd key tap behavior)
-	toggleModePersistent() {
-		this.#previousMode = this.#selectionMode
-		this.#modeSource = 'keyboard'
-		this.#selectionMode = this.#selectionMode === 'normal' ? 'rect-select' : 'normal'
-		// Note: Preserve current selection when toggling modes
-	}
-
-	// Revert temporary mode change
-	revertTemporaryMode() {
-		if (this.#modeSource === 'temporary') {
-			this.#selectionMode = this.#previousMode
-			this.#modeSource = 'button' // Reset to default button source
-			// Note: Preserve current selection when reverting temporary mode changes
-		}
-	}
-
 	// Get hierarchical children of a node
 	getNodeChildrenIds(nodeId: string, modules: FlowModule[] | undefined, nodes: Node[]): string[] {
 		const module = modules?.find((m) => m.id === nodeId)
@@ -203,13 +171,6 @@ export class SelectionManager {
 		if (event.key === 'Escape') {
 			// Escape key clears selection regardless of mode
 			this.clearSelection()
-		} else if (event.key === 'Meta' || event.key === 'Cmd') {
-			// Cmd/Meta key pressed - temporarily toggle mode
-			if (!this.#cmdKeyPressed) {
-				this.#cmdKeyPressed = true
-				event.preventDefault()
-				this.toggleModeTemporary()
-			}
 		} else if ((event.ctrlKey || event.metaKey) && event.key === 'a') {
 			event.preventDefault()
 			// Select all visible nodes (exclude note nodes)
@@ -219,13 +180,4 @@ export class SelectionManager {
 			}
 		}
 	}
-
-	// Handle keyboard releases
-	handleKeyUp(event: KeyboardEvent) {
-		if (event.key === 'Meta' || event.key === 'Cmd') {
-			// Cmd/Meta key released - revert temporary mode change
-			this.#cmdKeyPressed = false
-			this.revertTemporaryMode()
-		}
-	}
 }