Hi Ryan, make sure you're using the current version of the OBJ to 3DM converter, and then after you pick the file names for the conversion an options dialog will pop up at the end. It will have options for "One line for each edge" or "One closed polyline for each face". Make the second option active, the one for "One closed polyline for each face". then in the 3DM file each polygon in the OBJ file will have one closed polyline in the converted 3dM file, and then you can select all of those (ctrl+a) and run the Construct > Planar command to build planar surfaces from those outline curves. It will only work on polygons that were planar though, any polygons that were not fully planar you'll have to fill in manually.

However, this kind of conversion will result in one little trimmed planar face in MoI for each polygon in the original file. That kind of conversion will only work very well if the object is actually intended to be made up of planar surfaces like a box or a house or a diamond for example. If it's really meant to be a curved surface and it has some hundreds of thousands of little teeny tiny polygons in it that are trying to approximate a curved surface, it won't work very well. To get an actual smooth surface sheet from a big dense set of polygons is a much more tricky thing involving more specialized reverse engineering tools. Some of those are mentioned in this previous thread:
http://moi3d.com/forum/index.php?webtag=MOI&msg=4013.4
http://moi3d.com/forum/index.php?webtag=MOI&msg=1901.9

- Michael