What kind of canister filter is it?
If you can see that it's not full, then I'm betting it's a magnum, since they are the only ones with clear housings.
In most canisters, the water enters at the top and is pumped out from the bottom.
The way you solve this is to do the following:
1. Make sure the tank is full to the point where the return (to the tank) nozzle is submerged.
2. Shut the filter off.
3. Close both disconnect valves on the intake (or "IN") side of the filter (where water flows into the filter from the tank). Leave both valves on the output (or TO the tank) open.
4. Separate the closed valves so you have the "from the tank" hose hanging free.
5. Crack the disconnected valve on the filter just slightly. This will allow water to back siphon from the return nozzle back through the filter and will fill the canister, purging all of the air from the top through your open valve. When you see water rise to the top of the quick disconnect coupling, close the valve.
6. Reconnect and restart.