Can I get pop-up IFR clearance to waypoint (intersection)? Let's say I departed from the airport to fly to the practice area (VFR).
However, there is a thick cloud layer between where I am at right now and practice area. I already got a report that practice area is clear and VFR.

To go through the cloud, I need to request IFR to go through the cloud.
At this point, can I request pop-up IFR to any waypoint (as a destination) that is in practice area?

Will I be able to cancel that IFR flight right after I go through the cloud and when I am not in IMC?
Yes, you can file to a waypoint or navaid and can cancel IFR anytime you want. Whether or not ATC will grant a popup clearance depends on the facility and their workload. In places with a lot of flight training (Florida, Southern California), ATC, in particular the TRACONs, usually grants popups.