For my beaglebone userspace interrupt needs I use poll() mixed with pthreads. You can then give your interrupt it's own thread to block in and when the interrupt occurs you can then fire off whatever you wish to do.
If you need it done especially fast then you could always try spawning a new thread from your poll() in which to do your ISR and set the thread at a very low nice value and with a RT_SCHED scheduler.
Hope this helps!
Regards,