If Scan2CAD is informing you that your vector file contains unsupported 3D data, it is most likely because you are importing a DXF or DWG file containing a 3D model.
Scan2CAD is a 2D raster and vector conversion solution. It is not intended to support 3D vector models.
However some vector files may contain redundant 3D information (i.e. useless 3D data). In these cases Scan2CAD would process the rest of your vector design as you expect.