Resetting a dimension removes everything built there, such as portals and bases. Your Overworld is not affected, but your portals back may need to be rebuilt.

Paper and Spigot

1. Stop the server and open the Files tab.
2. Delete the world_nether folder (Nether) or world_the_end folder (End).
3. Start the server. A fresh dimension is generated.

Vanilla

1. Stop the server and open your main world folder (usually world).
2. Delete the DIM-1 folder for the Nether or DIM1 for the End.
3. Start the server.

If your world has a different folder name, check level-name in server.properties. Very new Minecraft releases may store dimensions in a different place inside the world folder, so look through the world folder for a folder named after the dimension if you cannot find these.

To reset everything, see Resetting your Worlds.