If you mean through arcpy and not calling some tool from the geoprocessing tools, you will have to look at the available methods in the geometry you are interested in. There are "cut", "intersect", "clip" and a variety of methods for geometries.
Whether they apply to annotation feature classes is another issue, since there is no particular case for that in the arcpy tree
Polygon—ArcGIS Pro | Documentation
... sort of retired...
