Migrate from innodb_file_per_table to off in MySQL
STEP #1

Set innodb_file_per_table to 0 in /etc/my.cnf

[mysqld]
innodb_file_per_table = 0


STEP #2

service mysql restart


STEP #3

Convert every InnoDB table to InnoDB again

echo "SET SQL_LOG_BIN = 0;" &gt; /root/ConvertInnoDBToInnoDB.sql
MYSQL_CONN="-u... -p..."
SQL="SELECT CONCAT('ALTER TABLE ',table_schema,'.',table_name,' ENGINE=InnoDB;')"
SQL="${SQL} FROM information_schema.tables WHERE engine='InnoDB'"
mysql ${MYSQL_CONN} -AN -e"${SQL}" &gt;&gt; /root/ConvertInnoDBToInnoDB.sql
less /root/ConvertInnoDBToInnoDB.sql


Once you view he script and are satisfied, login to mysql and run this

mysql&gt; source /root/ConvertInnoDBToInnoDB.sql


EPILOGUE

All .ibd files will vanish and all InnoDB tables and indexes will exist inside ibdata1

Give it a Try !!!