Is there a way to make him go away in some cutscenes? For example, if I just wanted a scene with the villain in it, can I achieve that?

What tool are you using? If it's rpgmaker 1 then just use character display dissapear.

for rpg maker 2 You can use party disappear

ah, well im using RPG Maker 2003 (i'm guessing that's the 2nd one). thing i'm a total newbie to the whole thing. where do i find this party disappear?

You use RM2K? Sorry, but this site is for RPG Maker (PS1), RPG Maker 2 (PS2), and the upcoming RPG Maker 3 (PS2) only (with one exception; see below). The RPG Makers downloadable for the PC were all illegally translated and put up on the net for free, which means the people who makes the RPGM series lose out on a lot of cash, so much so that there was never a legal PC RPGM release in the States due to the unlikelyhood of selling many copies when it was so readily available online for free.

There is only one way one could freely talk about any of the PC RPGMs here, and that is if you own a physical copy. You don't necessarily have to be using the copy (it's in Japanese, of course), you just have to be owning it and maybe supply some proof that you have imported a copy. I myself imported RPG Maker XP and have talked about my work on XP here, so I can safely say that this is the case.

i have never used RPGMXP but i have used RPGM1 and this is my idea
make an invable chaictor and put it in the cut sene where ever you want the camra to be at. hope this helps!