First enabling innodb_file_per_table and then when we optimize the tables, we can see that it creates .ibd files per table. Optimize table drops and recreates table so new .ibd files are created. Below are the steps:
Mysql> set global innodb_file_per_table=1;
Mysql> optimize table table_name;
Mysql> set global innodb_file_per_table=1;
Mysql> optimize table table_name;
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