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The 3D models that are the focus of your work in ZBrush are called tools. It's a little confusing why they would be called tools, but it comes from the fact that ZBrush was originally made to draw 2D pictures by stamping out copies of 3D models. Now that the 3D models are the focus of ZBrush, it doesn't make much sense anymore. But that's progress for you. Let's open up a tool to understand it better. Go down into the Light Box and open up the DemoSoldier project. We see in the Tool palette that this model is the active tool. When opening tools, you have to click and drag them out into the canvas and then put them into Edit mode.
When you want to save your work make sure that you save the tool, not the document. Some people might go up to the Document menu here and save it through here, but if you do that, you'll actually just save it to the image of the model rather than the model itself. To save properly, use the Save As button in the Tool palette over here on the right side. Tools are saved in the ZTL format. A new feature with ZBrush 4 is projects. Let's go into the Light Box and open up a project.
Notice that it just pops up without having to click and drag it out. Projects are the same thing as tools, but with the addition of saving document size, camera position, materials, colors, and other attributes along with the model. This saves you the effort of having to redo all those things every time you open a tool. It even saves whether or not a tool is in Edit mode, so you don't have to turn it on every time. To save and load as a project, go up to the File menu and click Open or Save As. Projects are saved in the ZPR format.
To recap, tools are the main way to work with 3D models in ZBrush. It's up to your preference whether you save as tools or projects. I prefer to use projects because of the additional settings that get saved along with them.
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