trimming/combining meshes question

Hello everyone, this is my first time posting, asking questions.

Really hope this will be an easy one. =P

So, basically, I have this crazy amount of mesh spheres traveling towards various points. As they travel along a curve (which is created by the shortest distance according to some mapping data), they grow bigger. Until they hit the destination. 

The problem is, how do I merge/trim/combine the meshes together when they overlap/touch each other? Something like what the Metaball does? This is all because I wanted to have a whole bunch of clean meshes as an end product so I can easily 3D print them or work on top of them as a new geometry. 

Thank you very much