diff --git a/src/bonsai/bonsai/bim/module/project/decorator.py b/src/bonsai/bonsai/bim/module/project/decorator.py
index 54a4e7181c..a2788bce09 100644
--- a/src/bonsai/bonsai/bim/module/project/decorator.py
+++ b/src/bonsai/bonsai/bim/module/project/decorator.py
@@ -26,6 +26,7 @@ from bpy_extras import view3d_utils
 from mathutils import Vector
 from gpu_extras.batch import batch_for_shader
 from bpy.app.handlers import persistent
+from typing import Union
 
 
 @persistent
@@ -92,14 +93,19 @@ class ProjectDecorator:
         selected_edges = []
         selected_tris = []
 
+        props = context.scene.BIMProjectProperties
         try:
-            obj = context.scene.BIMProjectProperties.queried_obj
+            obj = props.queried_obj
             selected_vertices = obj["selected_vertices"]
             selected_edges = obj["selected_edges"]
             selected_tris = obj["selected_tris"]
         except:
             return
 
+        root_obj: Union[bpy.types.Object, None] = props.queried_obj_root
+        if root_obj and not (m := root_obj.matrix_world).is_identity:
+            selected_vertices = [m @ Vector(v) for v in selected_vertices]
+
         if selected_edges:
             self.draw_batch("LINES", selected_vertices, selected_elements_color, selected_edges)
             self.draw_batch("TRIS", selected_vertices, transparent_color(selected_elements_color), selected_tris)
@@ -313,7 +319,6 @@ class MeasureDecorator:
         self.shader = gpu.shader.from_builtin("UNIFORM_COLOR")
         gpu.state.point_size_set(6)
 
-
         measure_data = context.scene.BIMPolylineProperties.measure_polyline
         for data in measure_data:
             polyline_data = data.polyline_point
@@ -327,7 +332,6 @@ class MeasureDecorator:
             for i in range(len(polyline_points) - 1):
                 polyline_edges.append([i, i + 1])
 
-
             # Draw polyline with selected points
             self.line_shader.uniform_float("lineWidth", 2.0)
             self.draw_batch("POINTS", polyline_points, decorator_color_special)
diff --git a/src/bonsai/bonsai/bim/module/project/operator.py b/src/bonsai/bonsai/bim/module/project/operator.py
index da7b472454..f391cdbdc8 100644
--- a/src/bonsai/bonsai/bim/module/project/operator.py
+++ b/src/bonsai/bonsai/bim/module/project/operator.py
@@ -1766,7 +1766,9 @@ class QueryLinkedElement(bpy.types.Operator):
         from bpy_extras.view3d_utils import region_2d_to_vector_3d, region_2d_to_origin_3d
 
         LinksData.linked_data = {}
-        bpy.context.scene.BIMProjectProperties.queried_obj = None
+        props = context.scene.BIMProjectProperties
+        props.queried_obj = None
+        props.quried_obj_root = None
 
         for area in bpy.context.screen.areas:
             if area.type == "PROPERTIES":
@@ -1781,7 +1783,7 @@ class QueryLinkedElement(bpy.types.Operator):
         coord = (self.mouse_x, self.mouse_y)
         origin = region_2d_to_origin_3d(region, rv3d, coord)
         direction = region_2d_to_vector_3d(region, rv3d, coord)
-        hit, location, normal, face_index, obj, matrix = self.ray_cast(context, origin, direction)
+        hit, location, normal, face_index, obj, instance_matrix = self.ray_cast(context, origin, direction)
         if not hit:
             self.report({"INFO"}, "No object found.")
             return {"FINISHED"}
@@ -1795,7 +1797,8 @@ class QueryLinkedElement(bpy.types.Operator):
         for i, guid_end_index in enumerate(obj["guid_ids"]):
             if face_index < guid_end_index:
                 guid = obj["guids"][i]
-                bpy.context.scene.BIMProjectProperties.queried_obj = obj
+                props.queried_obj = obj
+                props.queried_obj_root = self.find_obj_root(obj, instance_matrix)
 
                 selected_tris = []
                 selected_edges = []
@@ -1868,11 +1871,23 @@ class QueryLinkedElement(bpy.types.Operator):
         ProjectDecorator.install(bpy.context)
         return {"FINISHED"}
 
-    def ray_cast(self, context, origin, direction):
+    def ray_cast(self, context: bpy.types.Context, origin: Vector, direction: Vector):
         depsgraph = context.evaluated_depsgraph_get()
         result = context.scene.ray_cast(depsgraph, origin, direction)
         return result
 
+    def find_obj_root(self, obj: bpy.types.Object, matrix: Matrix) -> Union[bpy.types.Object, None]:
+        collections = set(obj.users_collection)
+        for o in bpy.data.objects:
+            if (
+                o.type != "EMPTY"
+                or o.instance_type != "COLLECTION"
+                or o.instance_collection not in collections
+                or not np.allclose(matrix, o.matrix_world, atol=1e-4)
+            ):
+                continue
+            return o
+
     def invoke(self, context, event):
         self.mouse_x = event.mouse_region_x
         self.mouse_y = event.mouse_region_y
@@ -2388,4 +2403,3 @@ class MeasureTool(bpy.types.Operator, PolylineOperator):
     def invoke(self, context, event):
         super().invoke(context, event)
         return {"RUNNING_MODAL"}
-
diff --git a/src/bonsai/bonsai/bim/module/project/prop.py b/src/bonsai/bonsai/bim/module/project/prop.py
index ae1412b8f2..0f9751df87 100644
--- a/src/bonsai/bonsai/bim/module/project/prop.py
+++ b/src/bonsai/bonsai/bim/module/project/prop.py
@@ -203,6 +203,7 @@ class BIMProjectProperties(PropertyGroup):
     library_file: EnumProperty(items=get_library_file, name="Library File", update=update_library_file)
     use_relative_project_path: BoolProperty(name="Use Relative Project Path", default=False)
     queried_obj: bpy.props.PointerProperty(type=bpy.types.Object)
+    queried_obj_root: bpy.props.PointerProperty(type=bpy.types.Object)
     clipping_planes: bpy.props.CollectionProperty(type=ObjProperty)
     clipping_planes_active: bpy.props.IntProperty(min=0, default=0, max=5)