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Inside view of the object with the protruding edge that I want to remove. Inner part of the object

Outside view of the object. The tubular portion intersects the body and results in the protruding mass that I want to remove. Outer part of the object

I have tried selecting around the intersection and using the Intersecting (knife) tool, but it always leaves behind unwanted artifacts.

selection: enter image description here

knife intersect tool result: enter image description here

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1 Answer 1

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First make sure you don't have any duplicate overlapping vertices and faces by going into Edit Mode with tab and then pressing AM > Merge By Distance. Then select only either the cylinder or the other object. In my case I selected the cylinder part and did Ctrl+F > Intersect (Knife). And it cut the mesh correctly.

enter image description here

However, I would not recommend boolean operation for your mesh as you can end up with ugly geometry that can become problematic. You can easily get a nice perfect quad topology, but first enable LoopTools via menu Edit → Preferences → Add-ons → LoopTools:

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Then select a nice edge outline with equal amount of edges as the end of your cylindrical opening. For example in my case I have a cylinder with 32 edges, so therefore I select a region on the other object surrounded by 32 edges. It does not necessarily need to be a square. You may need to experiment highlighting several sets of edges to find the perfect combination of the exact amount of edges as your cylindrical opening. Then go to menu Select > Select Loops > Select Loop Inner-Region.

enter image description here

Click RMB > LoopTools > Circle and then press i to inset faces and then X > Delete Faces. Now you have a beautiful hole to connect to.

enter image description here

Now select the edge loop of the cylindrical opening and the edge loop of the object you want to connect to and go to menu Edge > Bridge Edge Loops and increase Number of Cuts as needed.

enter image description here

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