1) Unzip mineways.zip, the whole thing, to some directory.
2) Double-click the Mineways program to run. Use "File | Open World" to select a world.
3) Use the left mouse button to drag the map around, use the mousewheel to zoom.
4) Drag with the right mouse button to select an area on the map and to adjust this rectangle.
5) Optionally use the middle mouse button or "Lower depth" slider to select a depth.
6) Export the model for 3D printing by "File | Export for 3D Printing..." - just hit "OK" on the Options dialog.
For Linux, download the Windows version and then use WINE to emulate Windows.
Not clear? Watch this quick introduction or this longer tutorial to see what's what. You can find more tutorials on the video playlist.
Problems? See the Troubleshooting Guide.
Exporting creates a .zip file by default. To preview your model, unzip the .zip file (there is also a checkbox on export, "Create files themselves", to avoid unzipping) and open the .wrl file with MeshLab or other VRML file viewer. If you want to 3D print your model, create a free Shapeways account and upload the .zip file. Once the model is processed by Shapeways (a few minutes), you can order it - make sure to select "colored sandstone" for the material. As an example, here's my non-profit store. Note that no part of this process will cost you anything, unless you actually order something.
What to try next: check out the "Export lesser blocks" feature, which lets you get more detail. This feature is not on by default because it has some risks - read up! To learn more about other options work through the documentation page, the information is pretty much in order of importance.
Super-fast quickstart for rendering: Same as for 3D printing export, but instead select "File | Export for Rendering..." - just hit "OK" on the Options dialog. You can preview the output OBJ file by using G3D, MeshLab, or any other OBJ file viewer. To import the model to a rendering program, see this area of the documentation.
Mac users:
Download Mineways for Mac. If you installed a previous version, you must use the Update:Uninstall.command file in this download to remove any previous version before installing - just double-click it. This program requires X11 for Mac OS X, which comes with the xcode tools, as found on the Mac OS X Install DVD. Xcode installation instructions can be found here.
Once installed, run Mineways. To load your world, use "File | Open..." You need to navigate to ~/Library/Application Support/minecraft/saves/, choose a world directory, and select the level.dat file there - see this video. If you can't find the Application Support/minecraft folder, open up the Terminal utility (Applications -> Utilities) and then type "chflags nohidden ~/Library".
If you are warned that the terrainExt.png file is not found, use "File | Set Terrain File" and look for it in Downloads/osxmineways or wherever you put mineways.exe. Selection is done with right-click; if you are using a trackpad or your mouse cannot right-click, hold down the Control key and left-click, or see this page for more options.
Older versions: If you are using Minecraft 1.1 or older, download v1.15 for Mac.