I've been watching a guy on twitch lately as he makes a custom map for his server that he's releasing on March 15th. He uses a program called RustEdit, which allows you to make a whole new map from scratch. If you're interested, I've left links below to the two videos that show him making a map.
I'm planning on messing around with this program to see what I can make, and if things turn out well maybe we can use it on our own Rust server.