For trousers, pleats don't run that far, they end down your thigh, trousers are hemmed all the way down at the leg opening. No issue there at all unless you're doing something crazy. The thing you run into there is taper, you may need to re-taper the trousers or you want to follow the current taper already in place. Sometimes re-tapering doesn't work because there's not enough fabric to make it less tapered. But in general, if you just want to remove a couple inches, no problem. Remember, most trousers are sold with 37" inseam and designed to be hemmed, regardless of being flat front, one/two/three pleats, forward or reverse pleat, etc.
