You can crop any loaded features to one or
more selected area features by first selecting the area feature(s) to
crop to, then right-clicking and selecting the Crop Loaded Features to
Selected Area(s) option. This will display a Crop to Selected Areas dialog
below), allowing you to choose which types of features to crop, whether
or not to mark the original features as deleted, and what layer to put
the cropped results in. 
Note that any features that are completely enclosed in the cropped area
and thus not cropped will just stay in their original layer.