It's very, very simple.

Open a folder using the Open button, then hit Go. The program will then generate a RomFS binary.

When it's done, it'll prompt you to save the binary with a file name of your choice.

RomFS-Builder

This is a program to convert a folder in windows into a 3DS RomFS binary. For use with makerom.

Credit to Project CTR, upon which much of the code used in the program is based.