Hi Skwerm, sorry I had missed that part about the indents being capsule-like.

So yeah the basic process will still be similar, you've got to try and model the capsule parts as some kind of solid object first and then use that to cut the main body with a boolean.

You're having some fillet troubles in this case because of a little tiny edge in your booleaned result here (looking here from below upwards):



Zooming in on that area you can see this little tiny edge fragment, shown selected here:



That little edge corresponds to the seam edge of the dome part of your capsule object:




That's going to be a problem for filleting, because the filleter is not able to totally consume an edge like that away, the fillet is going to be limited in size up to the point where it hits the end of that little edge, which is only a very small distance.

So you're going to want to get those dome pieces rotated around a bit so that when they leave their imprint they won't have such a small bit of edge left in the surviving piece.

- Michael