The integration of heterogeneous ontologies is often hampered by different upper level categories and relations. We report on an on-going effort to align clinical terminology/ontology SNOMED CT with the formal upper-level ontology BioTopLite. This alignment introduces several constraints at the OWL-DL level. The mapping was done manually by analysing formal and textual definitions. Descriptive logic classifiers interactively checked mapping steps, using small modules for increasing performance. We present an effective workflow, using modules of several scales. However, only part of the classes and relations could easily be mapped. The implications for future evolution of SNOMED CT are discussed. It seems generally feasible to use a highly constrained upper-level ontology as an upper level for the benefit of future SNOMED CT versions that are more interoperable with other biomedical ontologies.