Typically, flatness is a concern for a portion of the part, such as a sealing surface, an assembly plane.
To easily interpret flatness, the area of interest must be isolated by using layers or a path plot. Typically a coordinate system is set up so the out of plane direction is the Z-direction. Setting the direction is done with an anchor system or a local coordinate system.
In the figure below, the Sealing surface is in the XY plane, and is a very small fraction of the Z-deflection. Isolating the sealing surface to a layer helps in the interpretation.
A = Sealing Surface
If isolating the sealing surface is just above the tolerance, there is a possibility that the sealing surface is flat within tolerance but the surface is not in the XY plane. A command called flatness can be used to check a plane for flatness.
To use the flatness script: