Hello @Xam
What you’ve got here are just a number of issues resulting from trying to jump into Zbrush’s advanced features without learning the fundamentals first.
For instance, Dynamesh works best on meshes that are closed 3d volumes with thickness. Open volumes (holes), 2d, or overly thin geometry will tend to cause that swiss cheese effect.
ZRemesher is going to play a role in most retopo work where you want to create a low poly mesh from a high poly sculpt. However, hard surface meshes are a whole other kettle of fish, as they are still subject to the demands of subdivision, and must be creased in order to maintain a hard edge if you’re going to subdivide them again as you might as part of a texture creation process.
Also be aware that Zremesher will not fuse or weld any geometry. This must be done prior to Zremesher, with Dynamesh or Live Boolean.
Speaking of textures, your eventual output matters here. If working for texture or digital rendering in another application, your needs for quality low poly topology will be greater. If working, say, for print, then you could just dynamesh everything together (which will remove most of the overlapping geometry and fuse it), and then decimate to get the polycount down sufficiently for pre-print software.
Dynamesh would be very useful since it closes holes, removes overlapping geometry, and fuses intersecting geometry. In order to use it though, you’re going to need to find those problem areas of geometry and give them more thickness. OR, since it appears that the biggest problem pieces would be the open boxes, and they already have pretty decent lowish poly topology, simply separate these out from the more solid objects, and dynamesh everything else together.
Once you’ve done the cleanup work, and have a fused piece that has eliminated most extraneous geometry and fused it, you could send it through Zremesher to clean up the topology. Dynamesh will quickly create topology adequate for sculpting, but it does not create topology of the same quality as Zremesher.
Zbrush can definitely be used as a companion app to some other tool. But in order to get to that point you still have to put in the time to learn the program on a fundamental level before attempting more ambitious tasks. Be sure to check out the getting started sections of the Docs and the Pixologic Classroom, and work your way up to the kind of stuff you want to do.
Along the way, if you can focus on slightly more specific questions, we can be more helpful.
Good luck!
