Re: Subtract a tube from a wall
There are many requirements for booleans to work correctly. Both objects must be fully enclosed 3D shapes with no holes, and all normals facing outwards. After hearing that you had to remove so many duplicate vertices, I suspect the main shape is not perfect for this.
Try selecting Tools->select-leaky surfaces and seeing if anything is selected. It may be too much to fix so I'd suggest making the shape you want and moving that into position to replace the 'wall' where you want the hole area.
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