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.