I mask my parts with clear wide packing tape, and use it to close off the open ends.

The Ferric Chloride solution I use is a liquid. If you don't want to mask the entire piece, then there is an alternative method:

Get some latex gloves, safety goggles, a sponge, some FC etching solution, and a bucket of water. Mask your part as normal, then put on your gloves and goggles, and use the sponge to apply full-strength etchant to the exposed aluminum. Be careful, as spilling the etchant will leave stains or chemical burns. It's best to do this outside, to avoid buildup of toxic fumes. Dunk your part in the water when you are done etching, to stop the reaction.

You can get a visible etch after wiping the sponge over the part for a minute or two. Keep it up until you get the depth you're looking for.