Some flight planners will not let you delete waypoints from a SID or STAR without deleting the whole procedure, the argument being that if you do so you are not flying the 'true' procedure. I've always felt this is largely a bogus argument because real-world aircraft often don't fly the entire procedure and may be vectored off it for any number of reasons. If you need to remove a few waypoints from your flight plan and can't do it in the flight planner, you can manually edit the flight plan file, removing the waypoints and re-saving the file.
For the departure airport I think you get a warning if the waypoints are less than 10 miles from the airport. For the destination airport the warning may be at 15 miles but I would keep the last waypoint at least 20 miles out. When flying in Europe you leave the SID and STAR out of your PF3 flight plan in most cases because they are shorter and usually apply to a specific runway. In the US and Canada the SIDs/STARs are much longer and are used for multiple runways, so you will have some of the SID/STAR waypoints in your flight plan and eliminate those that are close to the airport.