The file mysql-bin.index keeps a list of all binary logs mysqld has generated and auto-rotated. The mechanisms for cleaning out the binlogs in conjunction with mysql-bin.index are:
PURGE BINARY LOGS TO'binlogname';
PURGE BINARY LOGS BEFORE 'datetimestamp';
These will clear all binary logs before the binlog or timestamp you just specified.

For example, if you run

PURGE BINARY LOGS TO'mysql-bin.000223';

this will erase all binary logs before 'mysql-bin.000223'.

If you run

PURGE BINARY LOGS BEFORE DATE(NOW()- INTERVAL 3 DAY)+ INTERVAL 0 SECOND;

this will erase all binary logs before midnight 3 days ago.

If you want to have binlog rotated away automatically and keep 3 days woth, simply set this:

mysql>SET GLOBAL expire_logs_days =3;
then add this to
/etc/my.cnf