EVERYTHING in the filter has bacteria growing in it. Trust us.
For my canister (which has 2 media trays), I siphon a bucket of water from the tank, turn off, disconnect the canister and move it to the sink. Take it apart, including removing the sponges from the tops of the media trays, take each media tray in turn and plunge it in and out of the water to rinse off any large particles (mainly plant leaves). I take each sponge and gently squeeze and swish it in the bucket of water a couple of times (apart from the white filter floss which gets a good hard squeezing because it's usually the dirtiest). Then reassemble.
There have been a couple of times when I've needed a second bucket of water from the tank because the water was a bit too dirty for my liking, but since I usually do a 20% water change at the same time (5-6 buckets) this isn't a problem.
Your first stage foam may have quite a lot of bacteria growing in it, since it should get the most/strongest water flow being first in line. I'm no expert, and while it may not be the case that everything has to be cleaned in tank water (I don't know enough to confirm or deny this), it's easier to follow our advice than constantly go through cycling issues in your tank if you keep wiping out your bacteria colonies. For a bit of extra work you'll have a healthier tank, and isn't that what it's all about?