When I try to edit the vtf file for the cube's skin, everything is transparent, (in paint.net with the vtf plugin) everything looks fine in vtfedit.You can look at all the images in the top corner:

Screenshot (20).png

Open .vtf file in VTFEdit and export it into .png image. Then open that image in your image editor and do with it what you like. Go back to VTFEdit and import your new image.

The alpha channel is used as the selfillummask. Turn it off.

@JoeyGuy917: You should understand how textures and their 'channels' work in the game. If you open that texture into VTFEdit, you'll find that you can choose to see the image filtering its channels. The important here is the alpha channel. The game uses the alpha channel in many awesome ways via the shaders. One example is the self-illumination, if you add the parameter 'selfillum 1' to your material file (.VMT), you'll be telling the game to use the alpha channel as a "map" of how to backlight the texture, what parts should be spotted and which ones not.

If you open that cube skin texture into VTFEdit, you can go to the View menu and select to see only the alpha channel by ticking 'Mask' (you'll end up seeing exactly what your screenshot is showing, by the way, update Paint.Net to 3.5.11 :p), or to see the whole texture. If you want to edit one stock texture, export it first to .JPG. Then open it in Paint.Net and work with it.

Once you have finished with it, you can create your alpha cbannel. in Paint.Net is not as straight forward as in PS, it's more complicated, but send me a pm if you need help on that

One more quick question. On more complex models, how would you know which part of the texture is which?

EDIT: Another question, would I need to export the model too?

JoeyGuy917 wrote:
One more quick question. On more complex models, how would you know which part of the texture is which?

Well, what you ask is known as UV-mapping. This is how the modellers tell the modelling program how to texture (and what texture file to grab it from) each bit of the model. This is complex and will take you some time to learn.

But in order to know the variety of textures that one given model uses, you can use a hex editor to open the .MDL file and "see inside" the model. For example, the cube:

If you scroll down to the bottom of the window you'll find a lot of understandable letters: first you'll find the model properties, then the model name and its path, etc. Then you'll find all the textures the model uses, and then the path to the materials folder (only in the case that ALL the textures are under the same materials folder, for more complex models, you'll have several paths, but preceeding the material texture names)

BE CAREFUL WITH WHAT YOU EDIT WHEN USING A HEX EDITOR BECAUSE YOU COULD TURN YOUR MODEL USELESS!

You can now open each of them to check all the textures that the model uses, and identify what parts of each texture you recognize on the model; many times you'll find multiple skins for the same model.

JoeyGuy917 wrote:
EDIT: Another question, would I need to export the model too?

I don't know what exactly you are trying to achieve, but if you are just making one custom texture for the weighted cube, you'll need to make the model to point to your custom texture, therefore you'll need to extract the model, yes. Then I'd recommend you to hex the model (to edit it into a hex editor), it's the easiest way to have your custom model using your textures. Take a look to this thread about hexing a model.