What to use to fill in small holes in metal

I think you should post a pic of said area so people can give you better options of what should be done.

things such as porosity can be addressed by cleaning the metal up well and then coating it with a rust dissolver and a rust inhibiting primer.

and using a good high build primer can take away most if not all the imperfections associated with minor porosity.

such things like rot should be cut away and replaced with a patch panel or a replacement body panel.

minor imperfections ( done the right way ) can be gone over with bondo .....however....if you don't care about the car and just want it to "look" like its ok......you can stuff the hole full of auto trader magazines,chicken wire,window screen,cover with duct tape and then bondo over it.... ( don't ask.....had a mustang I gave 2 $h!ts less about at one time HAHAHA).

if it has pin holes and holes and the metal is soft feeling (can flex the metal when putting pressure on it or dent it in when putting pressure on it) than I would suggest cutting out the questionable area and welding in a patch.