If I filter my beer can I still bottle condition?
If you are using a filtration system, then you should just force-carbonate your beer. The best and quickest way to filter and carbonate is to keg your beer.
How to Filter and Carbonate Your Home Brew
If you plan to bottle condition your beer, filtration is not recommended. If, however you really want to filter your beer, you can re-prime the beer by adding a very small amount of highly flocculant yeast I (such as Nottingham) to your bottles.