here is something I did to do exactly what you wanted...
(altho i needed my insert statements in MySQL to transfer parts of some tables to an Apache server. So the syntax might vary).
'INSERT INTO `db_name`.`table_name`
' , [col1] , ','
, [col2], ','
, [col3], ');'
where col5 = 'some condition';
Then u can right click on the results and save them as... CSV file.
Then open the CSV file in notepad++ and replace all the double quotes " with nothing.
And volah I had 7000 insert statements to run in mysqlworkbench and transfer only the specific columns I needed to a different database.
You can use workbench or mssms to generate the insert statement for the destination table as a starting point by right clicking on the table in either program and copy to your select statment.
The beauty of this method also is if your destination where you want to run the inserts might have different column names to the source.