You receive a warning if PF3 waypoints are closer than 5 nm to each other. Having waypoints that are too close to each other may or may not cause problems (see p. 34 of the User Guide for more info).
Waypoints too close to the airport are a more serious issue. The warning for waypoints too close to the departure airport is 10 nm and to the destination airport it is 15 nm. Waypoints closer to the airports than these ranges should generally be left out of your PF3 flight plan because you will be vectored at these distance ranges. I try to avoid having any PF3 waypoints closer than 20 nm from the destination airport, and having a last waypoint at about 25-40 nm works well. If a procedure requires that you fly waypoints that are very close to the airport, enter them in your FMC and fly a SID or STAR in PF3, but do not include the close waypoints in your PF3 flight plan. See the following for more info:
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