After importing the OBJ file and using the Trapcode Form plugin, I get the After Effects error: Form OBJ Error: Illegal obj fail (1) (25 :: 241) error, I uninstalled Trapcode and reinstalled it but again I get the same error. I need your help.
Entirely depends on what 3D program you use. Some have "separate/ split meshes" functions, others will require to select individual polygons and copy & paste them to new layers/ objects or to invert the selection(s) and delete unwanted polygons. The number of meshes doesn't matter. An OBJ file is just one huge lump of polygons and vertices. It's more likely that the sheer number of polygons could be an issue, that there is "bad" geometry in the file or that it contains invalid entity info like e.g. proprietary custom info that some 3D programs store as comments in the file. Impossible to know without any info about the source and nature of your files.