Please share a screen shot, it will help us to understand.
There are a couple things you could do. The easiest might be to write the filter into your SQL join. Something like:
WHERE EMAIL IS NOT NULL
But this is a connection to salesforce - not a sql server - maybe you can't filter down salesforce data for an extract? Has anyone successfully filtered salesofrce data prior to extract of data?
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This answer is incorrect. Salesforce connect does not allow to add a filter onto the extract pull. You may add data source filters after the extract but they only hide data. You still must carry that data hidden in the file and when uploading to the server.