Best way to "sculpt" sphere-shaped holes on a sphere surface? Sorry for the confusing title, the best way to explain it is to look at my image (don't pay attention to the lines connecting the holes and sorry for the poor quality)

I have been thinking about this for a while and I can't think about a good way to do it. Booleans would result in a very glitchy topology and very bad results when subdivided, sculpting it wouldn't be precise enough (for me) and modeling it poly-by-poly would probably take forever, not to mention quite challenging.

There is surely a good and simple way to do it, but I just cannot think of one.
If you use booleans and want smooth spheres as results, increase your original sphere segment counts, later on you can always retopologize if the resulting face count is too high. Starting from a highpoly mesh and working to a lower one can give acceptable results.

The implementation of Blender Booleans is from the Carve Library, this is what the blender dev has to say about how to use booleans (in another very similar question) -- link



The carve library has made it possible to do really nice booleans in blender, but you need sufficient geometry for the polygon based approach to retain smooth shapes.

Cleaner topology results come from being precise about matching up the level of sudivision where the objects interface each other. Taking a highly divided sphere like above and doing a difference with a scaled down sphere with identical vert count will produce more geometry than needed.

Ideally you will have similar face sizes like here:



Use the EdgeSplit Modifier, on smooth shaded faces, in combination with matching face sizes it looks acceptable.