There are definitely solutions. To start, what brand and model filter do you have/will you be getting? Some filters shold have stock input/ouputs that are long enough. If not, options for what can be done kind of depend on what canister we are talking about.
If it is a Fluval, Hydrophyte (a member here, and owner of Riparium Supply) has done some modification to his. I am sure he will chime in pretty soon here.
If it is an EHEIM, I believe that they sell some cheap input/outputs that are much longer and better than the stock ones. Here is a link to them if you want:http://www.drsfostersmith.com/produc...fm?pcatid=9606
Those may work.