Remove Intersecting Mesh between multiple objects


I have a fairly complicated mesh that I need to simulate using rigid body dynamics. The problem is that since each part is slightly intersecting, when I simulate it in any software it explodes. Is there any way to boolean out the intersecting parts of the mesh so that none of the individual parts are clipping? Do you know of any software that could do this easily without painstakingly applying booleans to each and every object? Thanks


You should share more info, such as showing the actual objects, are they simply intersecting each other or “fused” together? Where do they come from? Is retopology a viable option? Which software is used for the simulation.