MySQL - Manipulating MyISAM files directly brings down entire database
You had setup MySQL Replication, you could achieve the following:
SLAVE
You could do the following on the Slave in Session #1
mysql&gt; STOP SLAVE SQL_THREAD;
mysql&gt; FLUSH TABLES WITH READ LOCK;
mysql&gt; DO SLEEP(86400);

NOTE: Doing STOP SLAVE SQL_THREAD stop SQL processing but continues collecting binary log events from the Master.
Open another session (Session #2) and copy the .frm, .MYD, and .MYI files to your heart's content as you stated in the question.
When you are done copying the files from the Slave to the target server, simply kill the sleep session in Session #1 and mysql session. Log back into mysql and run
mysql&gt; START SLAVE;

Doing it this way assures that all the MyISAM tables are from the same point-in-time.
MASTER
The Master can keep on going with all the reads and writes.