I was wondering if it is possible to place terrain tiles that are transparent but block the vision/movement of units on normally passable terrain. I am using ScmDraft 2 and have Extar editior and starforge, do any of these programs have these type transparent tiles? If not can I make them, and with which program?

Afaik, it's not possible without modding. You can block movement by neutral dark templars, though.

Perhaps use high terrain with a clocked unit wall infont of it...

Yeah, that'll work if you make sure that the unit cannot get over high terran. Some doodad tiles also do block view.
There's a small chance also that you find a null file that has set the block view flag, but I doubt there's any, plus it wouldn't look good.

I know some doodads that block vision, if you want them tell me.

Well, the basic concept is to turn high dirt on the jungle tileset into caves (in other words you cant see off the sides of cliffs). Is there any way to edit the properties of the terrain (like maybe the edge pieces of the cliff) to block vision? Otherwise I'm just gonna have to go with boring ole dirt floor caves, or make blocky interiors. :-\

Dirt floor caves?
Clearly, mud tiles are superior for cave interiors.
Damn, that almost rhymed -_-

With some good blending it can be really easy.

Again, there's no way to modify the terrain properties without moding the SC engine, and that would mean that noone would be able to play your map over bnet if you don't send them the mod before.

That may work....

Wrong clokr if he made it a modded map they could just use scm loader to play it .

No one plays with SCM Loader for the heck of it, I hate it when people say that like they do.

You can use extended terrain to make the top of the cliff dirt, rather than high dirt.