I think removing the canister filter is a great idea I found that they just collect to much crap and cleaning them became a pain. But first I would make sure that your bio-bottle is fully cycled before removing the canister bio-bottles usually take about six to eight weeks to really get going. The reason it takes so long to seed is they are self cleaning which is the best part and the worst part (when starting a new bottle). When it gets going you will really love the simplicity of the filter.....Josie