If your are using Blender to make stl's for your prints then consider activating the "Mesh 3D Print Toolbox" in preferences.The plugin can be download here.
The little white arrow pointing to the right is a drop down that should also give you access to the documentation for it as well.
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Dont forget to save your settings!
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Once its activate you have access to the "Check all" and "Make Manifold" button which can help you make sure your models are water tight.Once you're finished you can then set an export directory and export your file as an STL ;-D