Not sure what you mean by point file vs. line file, but basically, Maemo Mapper supports the concept of a "route" (which can be downloaded from the internet), which is a bunch of connected points that describe directions from point A to point B. What Benson has suggested is to create a "route" that represents the polygon for which you want to download maps, then use the "Along Route" option in the "Manage Maps" dialog to download maps along that polygonal route. You'll have to fill in the polygon with more route points to download maps for the whole polygon (as opposed to just the perimeter), but it should be possible.

Edit: to clarify: Maemo Mapper downloads all of the maps needed along the route, including the maps that are between two route points. So, for example, you could create a route with two point, one in New York and the other in San Francisco, and Maemo Mapper will download all of the maps in a straight line between those two points. Likewise, your route could be composed of three points in a triangle (plus a fourth point to "close" the triangle), and Maemo Mapper will download maps along the perimeter of the triangle. To "fill" the triangle, you'd have to add route point inside it, either with concentric triangles, or with some other pattern.