Finding good trails in the Bitterroot can be a bit of a trick. Most of the canyons are best left to hikers because of extensive rock; but around the periphery of the valley there are some great rides. Making loops takes some investigation and usually some strong legs and lungs, but one of the best loops has got to be Lake Como.
If the circuit around the lake does not give you enough there are other trails in the area along both ridges both south and north of Lake Como. Accessed in a variety of ways including off the forest roads there are great smooth trails and old two tracks through the forest to make for up to a full day length ride without ever substantial uphill vertical gain. With lots of views of the lake from many sweet spots, this has got to be the best place for mountain biking in the heart of the Bitterroot Range.
For the more aerobic and climbing centric cycler there are some great rides up Warm Springs Creek, highlighted by the Warm Springs Ridge to Fire Creek trail, a 3000' climb followed by an exciting descent to Warm Springs Creek. With additions to this ride, this may be the best place to get in really good shape and has lots of loop and figure eight options with big vertical, dirt trails, and at this point quite cleared out by the local Hamilton mountain biking club.