All skimmers have key features in common: water flows through a chamber and is brought into contact with a column of fine bubbles. The bubbles collect proteins and other substances and carry them to the top of the device where the foam, but not the water, collects in a cup. Here the foam condenses to a liquid, which can be easily removed from the system. The material that collects in the cup can range from pale greenish-yellow, watery liquid to a thick black tar.
Consider this summary of optimal protein skimmer design by Randy Holmes-Farley: 
Also under considerable recent attention has been the general shape of a skimmer as well.  In particular, much attention has been given to the introduction of cone shaped skimmer units.  Originally designed by Klaus Jensen in 2004, the concept was founded on the principle that a conical body allows the foam to accumulate more steadily through a gently sloping transition.  It was claimed that this reduces the overall turbulence, resulting in more efficient skimming. However, this design reduces the overall volume inside the skimmer, reducing dwell time. Cylindrical-shaped protein skimmers are the most popular design and allow for the largest volume of air and water.
Overall, protein skimmers can be classed in two ways depending on whether they operate by co-current flow or counter-current flow. In a co-current flow system, air is introduced at the bottom of the chamber and is in contact with the water as it rises upwards towards the collection chamber. In a counter-current system, air is forced into the system under pressure and moves against the flow of the water for a while before it rises up towards the collection cup. Because the air bubbles may be in contact with the water for a longer period in a counter-current flow system, protein skimmers of this type are considered by some to be more effective at removing organic wastes.