I followed steps to make an ellipse with multiple regular holes using cylinders (picture on left). How do I remove the internal cylinders from the ellipse (picture on right)?
I ideally want to end up with the ellipse hollow with a 1cm lining
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If you model the cylinders as a separate object, you can use a boolean modifier on the sphere/ellipse to 'subtract' the cylinders. Then, if you turn off the cylinders (you don't have to delete them), you'll have the sphere/ellipse with holes where the cylinders should be.
I don't know any better way to do it than the following (and I assume this is all one object, with all the vertices merged. If not, there's a simpler option):
Go into Edit Mode for the egg-shaped object and also activate Face Select mode. Alt + select any face of any cylinder where it meets the egg's outer shell. This will select all faces in that cylinder, or at least, all of the faces which would make up a face loop that is nearest the shell. Now delete them (x, then from the Delete Menu, Faces). If any part of the cylinder remains, leave it. The important thing is that it's no longer directly touching the egg object.
Now repeat the above steps for the next cylinder (Alt + select the face loop which meets the outer shell, and delete that part which meets the shell). Continue until the outer-most face loops for all cylinders is deleted.
If your topology was such that the above process got rid of all inner parts, you're done. If not, continue below.
While still in Edit Mode, press p and from the Separate menu, choose Loose Parts.
Now go into Object Mode, select some part of the inner structure which remained after the previous steps (if you did everything right, it should select the interior as one whole piece. If it won't select, examine the mesh for signs of incomplete or botched separations), and delete it.
When this is all done, go into Object Mode and click on the Modifier tab of the Properties Panel. Choose to create a Solidify modifier on the egg shell object. Choose a thickness that suits you.