Sure. There aren't many guides specific to it but Booster's Lab is capable of it. I can give you a few quick instructions to get you started.
1) navigate to C:\Program Files (x86)\Steam\steamapps\common\cave story+\data
2) make a copy of the base folder and name it to something else
3) add your mod to mods.txt
4) using Booster's Lab, go to your new mod folder and open stage.tbl
5) mak moad
1) navigate to C:\Program Files (x86)\Steam\steamapps\common\cave story+\data
2) make a copy of the base folder and name it to something else
3) add your mod to mods.txt
4) using Booster's Lab, go to your new mod folder and open stage.tbl
5) mak moad