To crop the size of the currently displayed map layer, first enable the select area mouse tool, and left-click and drag to select the desired area (see below). Note that the status bar displays the start and end coordinates and the size of the selected area.
Once you've roughly selected the area you wish to keep, select the 'Layers→Crop' menu item. This will open the 'Crop map layer' window, shown below:
In this window, you may set the exact coordinates to be cropped. The initial values will be those of the area selected using the select area mouse tool. Once you click OK, L3DT will crop the map to the area selected.