Coping with shallow depth of field
When you're shooting at the minimum focus distance, depth of field is extremely small. For example, with a 100mm lens on an APS-C camera, it's just 0.6mm at an aperture of f/2.8, so only areas that are within 0.3mm in front of or behind the focus point will be rendered sharply. Even at f/11, the depth of field is only 2.6mm.
Shallow depths of field aren't too much of a problem when shooting flat two-dimensional objects, but things get tricky in 3D.
Because focusing is so critical, you're usually best off switching to manual focus, so you can focus on exactly the part of the object you want to be sharp.
Fixing the camera in place and using Live View is helpful, as you can select a magnified view on the camera's LCD for high-precision focusing.
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