How to Clip a Set of Polygons Down to a Polygon Area

Load the Geoprocessing Extension

Create the polygon theme that you want clipped.

Create a new polygon theme with the shape of the area to be clipped.

Run the Geoprocessing Wizard (under the "View" menu).

Choose: "clip one theme based on another."

Next: select "input theme to clip" to be the polygon theme you want to clip.

Select "polygon overlay them" to be the polygon theme with the shape of the area to be clipped.

Specify an output file. Be sure to put it in your directory.

Press Finish.

It should create a new clipped theme.