You should be able to remove the old filter with out any problems. If you want to be doubly sure tho, it is a good idea to add the media from the old filter into your new canister filter, so you are on the right path with that idea!
Often times when I have to quick start a tank I will take media from an established tank and use it to seed the new aquarium. I set my 55 gallon aquarium up in one evening and added my Red Devil Cichlid, I ran a seeded filter and started with 20 gallons of established and clean aquarium water, with my 75 gallon, I waited two days because the water was cloudy from the substrate. Both of these tanks have been up and running for a couple years now, so they have an established bacteria population in the substrate, so when I have to move I simply save ten gallons from each tank and then set it back up the same day and put my fish back in, I've never had a problem so far.