Sensible data management tool for importing and exporting of large data files
It sounds like you should check out MySQL's load data infile ....  The docs claim that it is a very fast way to load rows. (I personally have never loaded millions of rows at once).

Once the data is loaded, you may need/want to add appropriate indexes to your tables to help speed up query performance.  

For getting data out of MySQL, check out select ... into outfile.