This tutorial teaches how to set up a multi battle system similar to the one used in Final Fantasy Mystic Quest, where you can clear out certain areas (represented by crossed swords in the game). It’s a simple method that can easily be adapted for your game.
For convenience, the demo can be downloaded for quicker installation and study. This is a complete project, including the RTP, so it is quite large. You can extract it directly into your RM2K3 Projects folder.
The Final Fantasy Mystic Quest Battlefield System Tutorial, along with the downloadable demo, can be viewed here.