Transparency in FSO is tricky. It's tied to object hierarchy and... something else, as well. With simple stuff, it's easy to do, but if you want things like entirely transparent ships, it becomes a bit more difficult.
At the top of the screen in F3 Viewer you have Render Options. You have to deselect some option. I don't remember what was it's name.
He's not asking about F3 view, he's asking about getting transparency right. He likely enabled this view on purpose, it makes the whole ship transparent (I don't know what it's good for).
Not anymore, it's not. Well, it is but you don't have to think about that anymore. If you have a texture with transparency, name it 'SOMENAME-trans'. (You'll then have 'SOMENAME-trans-glow' or whatever. Then make sure your diffuse -trans texture has an alpha channel. That should do it.
Though, you'll need to make sure to model whatever is being the transparent texture is it allows viewing into the ship. Clear Lego bricks should probably have modeled bricks or Lego people behind them.
NOTE: Last I did this, it did not look right in PCS2, but FSO was fine.
EDIT: The transparency option in the F3 Lab is unrelated to creating transparent glass (or bricks) on ships. Just FYI.