To quote directly from the
FEATool quickstart guide:
"FEATool Multiphysics does not prescribe or make users use a specific unit system, it is therefore up to the user define and use consistent units. If for example a geometry length unit is chosen as meters (m), then standard SI-units are recommended for the equation and boundary coefficients. Using another length unit such as millimeters (mm) or inches, will typically require corresponding rescaling of model coefficients to preserve unit consistency."
So in your case if you geometry/CAD model is in "mm" then yes your other coefficients and material parameters would have to be defined using [mm] as a base length scale.