|Crape myrtles bloom on the new growth of the season so the best time to prune is in the late winter or very early spring. In general, you'll want to prune all of the tops stems down to about 6 inches or so above the intersection where the stem meets a branch. Two new stems will emerge from beneath your cuts. By using this method of pruning you will be promoting twice as many branches every season - which means a fuller canopy and twice as many blooms. To further "clean up" your crape myrtle tree, you can prune suckers that grew from the trunk base, and twiggy growth that emerged up and along the main trunk(s).
Here's what I do: Trace down from the top of a stem (from the seedpods if the tree bloomed last year), to where that stem meets a branch. Using a pair of sharp bypass or lopper pruners make a cut about 6 inches or so above the intersection - never below the intersection. The 6" stub that is left will be strong enough to support the new branches that emerge just below your cut. (Another method for pruning the top stems is to grap the top of the stem gently bending it over and make a cut where the stem begins to bend at the point closest to the intersection.)
Best wishes with your crape myrtles.