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In MS/SQL I have a table with multiple geometry fields. When using a FeatureReader, how can I designate which geometry column to read ?

I believe you'll have to check the option "Handle multiple spatial columns" on the reader. You can then select the geometry column by filtering on the traits in the resulting aggregate, see also the documentation:

http://docs.safe.com/fme/2020.1/html/FME_Desktop_Documentation/FME_ReadersWriters/mssql_spatial/MSSQL_Spatial_reader.htm

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