Remove InnoDB files (ibdata1 and iblog files) after migration to MyISAM
In case you do not have a single InnoDB table, then yes, you can remove the ibdata file and the ib_logfile[01] files.

However, note:


With MySQL 5.6 there are system InnoDB tables, which means you don't want to remove the InnoDB files ever.
It is best done when the server is stopped.