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What @mdahlhausen said. Instead of pulling a window off the base surface to extrude it, slice your wall into orthogonal subsurfaces that define the rectangular opening(s) you wish to extrude. Then pull those subdivided wall elements, and once extruded, draw your window rectangles on those. And as @mdahlhausen said, make sure the windows are offset from the edges of these new, extruded base surfaces. The offset tool is great for this.