The primitives provided by the SCAD language, in particular the minkowski() operation, can be used to automatically add fillets to every concave seam of a piece.

However, the operation is expensive and probably not a feasible way to approach things.

This scad file shows a shape made of three interlocking cuboids and a cylinder filleted using a very polygonal sphere. A finer-resolution sphere would produce a far better result, but on my middle-aged macbokk would take hours or more to compute.