The first thing is to make sure whether you're dealing with a single surface. Scans (think this is some kind of surface reconstruction) often own outliers (small surfaces not connected to the either surface):
Run EDIT/SeparateShells on your source mesh. If MM finds several shells discard all but the either surface.
On this single surface start (do NOT do AutoRepairAll on a single sided surface) Inspector. If there's only a single blue marker sphere all is fine and Cancel Inspector.
If there are more markers either: Click all the spheres but the one pointing to the outer boundary one by one to fix the detected issues (unfortunately there's no RepairAllBut the outer boundary).
Or: Switch of texture rendering by dragging the default shader (next to the + ) from SHADERS onto your object for a better view of face groups (your texture is still kept). Make sure you're on MeshColorMode= GroupColor(Default) (see Preferences). Now SELECT a piece at the boundary of the mesh and do Modify/CreateFaceGroup. If there are more than one group at the boundary Inspector will fill the hole with a new face group. So you might do AutoRepairAll in Inspector, go to SELECT, select this infill group by double click and discard it.
Now a planar cut of a single surface without inside errors might still result in problems if there are undercuts cut by PlaneCut due to surface noise. E.g. at extreme:

If you'd do the cut in CutType=Slice(KeepBoth) and you'd do Separate after that cut the upper example will result in 5 objects. Although it's not ideal one might solve this doing PlaneCut in CutType=SliceGroups. This results in this:

Now SELECT the main group (e.g. the white one) by double click:

Hit Y to separate:

Now there's a non connected piece at the brown side (the undercut closest to the viewer). So make the brown object the active one and do EDIT/SeparateShells:

Activate all the split parts from brown + the white object, run Combine and finally EDIT/CloseCracks on the combined object. Now there are two objects only (transformed for a better view):

Note about MM's texture handling:
As soon as MM needs to "invent" textures by interpolation it creates a second texture image for areas where it could not simply split existing faces and it's texture snippet along. Seems your target application doesn't support more than one texture per file. So you need to find an app joining several textures to a single texture map. MM doesn't do this.