3D manufacturing is not as automated as 2.5D manufacturing is.
3D Milling tool selection is governed by the Tool diameter and Tool end radius settings in the Surface Mill tab of the Default Attributes (open Default Attributes by selecting Default Attributes in the Manufacturing menu). FeatureCAM uses that tool to manufacture the part unless you override the selection on a feature by feature basis.
In areas where the tool fits, the surfaces are milled within the finish allowance up to the tolerance setting for the surface feature. If the tool is too large to fit in the more constrained areas of a surface, that area is left unmilled. If the surfaces contain a gap smaller than the tool diameter, that gap is bridged by a straight line.
The feature is milled up to the check allowance for any check surface(s) set with the feature.