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Understanding laser focus will help you reason about difficulties that you are having with cutting your material. Here is a diagram of a general lens mfor a laser cutter:

As the diagram indicates, material surfaces that are placed above or below the focal point will have a larger cutting area than the potential minimum size. A larger area means the same energy is dispersed over a larger area, and therefore may not create as deep of a cut as you are expecting.

For thicker materials, the focus length problem can become more obvious: