If you are talking about Metal-organic framework analysis then TEM as it differentiates phase by density gradient. Law density (Organic) bright, high density (metal) dark.
In your question you say SEM or TEM for MOF identification. Do you want to identify what? Grain sizes? Crystallite sizes? The crystal phase? In this last case you need to use electronic diffraction of TEM (from SAED) or HR-TEM...