Launch After Effects and click "File," then "Import." Upon clicking this, the downloader will scan for storage devices connected to your PC. Select your video camera from the drop-down field at the top of the dialog box and choose a disk location where the photos will be stored. Finally, click "Get Photos."
Click "File" followed by "Open In Camera Raw" after the files have downloaded onto your machine. This allows you to edit the raw footage that After Effects will reference. Be aware that changes you make to your raw footage will effect all the clips in your After Effects project that use that raw footage.
Select the "Crop" tool from the "Camera Raw" dialog box. It looks like two "L" shapes, one inverted, overlapping to form a square. Drag a box over your preview window, don't worry if it isn't right straight away, click and drag the small nodes on the border of your selection, this will allow you to edit the box you have drawn.
Double-click in the preview window once you are happy with the cropped area. The dimmed area outside the crop-box will be discarded. Save changes with the "File" menu if satisfied.