Minecraft texture bug?

I have just tried to make my own texture pack for Minecraft for the first time. So I pulled the standard textures from the MC files and started to completely re-pixel the texture in Paint.net (NOT Paint). Then I saved it and dragged it into the texture pack that I created. Then I looked at the item and the texture was there! Only it was completely 2D in the hand or had no depth like all other items. (See image)

Now I wanted to ask what did I do wrong? Where is the problem? I really need your help!

You have done nothing wrong. However, you mainly used the same colors. In a 16x16 texture it is difficult to bring in shadows etc. Use the same color on the edge, but a little darker, then it should look a little better. And by the way, Paint.net is Paint. (Most people just don't say ".net" to it.)

But even that is of little use to me when Minecraft displays the model completely flat, other objects are about 1 pixel deep.

By the way, Paint.net is Paint

When you just say "paint", a lot of people mean MS Paint.

Only marginally. ^^

Did you use a different texturepack as a base? If so, what does the sword look like there?

You didn't do anything wrong. The same problem is explained here:

Remove all other texture packs. Hope I could help you?

I pulled the standard texture pack from the files myself and then re-pixeled it in Paint.net.

I can't take them all out, I only have my own inside.

And by the way, Paint.net is Paint. (Most people just don't say ".net" to it.)

Not correct. Paint is Microsoft Paint that can't even work with layers.

Paint.net has been around since 2004 and is developed by Rick Brewster.

Oops. My mistake.