Photoshop
You can create new blank layer which is transparent by clicking Create a new layer (page) icon in LAYERS palette or from Layer > New > Layer (Ctrl + Shift + N). To make existing layer transparent or with some level of transparency (0% - transparent, 100% - opaque) use Opacity slider (or type number in text field) in top right corner in LAYERS palette. Another way to make layer transparent is to remove its fill using Fill slider which is below Opacity (click triangle on right side to appear slider). Difference between this two methods which may seems to you as exactly the same is because
Photoshop does not treat layer effect as layer fill so you can for example add Drop Shadow layer effect to an object (circle for example) and setting Fill to 0% will remove object fill (will make it invisible) but drop shadow will still be visible, on the other hand setting Opacity to 0% will hide (make transparent) and object and layer effect.
