The uri parameter of "Enterprise Architect Application" reader can be used for selecting a specific package to read. Two format of uri are allowed:
{e3b53655-c00d-4368-beda-eda6772439d7}EAPK_e3b53655_c00d_4368_beda_eda6772439d7
Model umlModel = ...
Map options = ...
umlModel.read("Enterprise Architect Application", "{e3b53655-c00d-4368-beda-eda6772439d7}", options);

Reading UML Data
Reading Enterprise Architect Data
MDAccess for UML API Reference
MDAccess for Enterprise Architect API Reference