Can be done using phpMyAdmin, but you need to go back through your notes that you made when you installed all the extra add-ons...
(You did keep notes, didn't you? ... of course you did! How silly of me to even ask the question...)
Anyway... some add-ons may make changes to the dbase, others may not.
Any add-on that required a SQL patch will have made changes to the database.
If you have a record of all add-ons, you will only need to concentrate on those that make dbase changes.
First thing is to make a COPY of your database - because you will tinker with the COPY and not the original. You do this by creating a new empty database with full user permissions in your cPanel, and then using the OPERATIONS tab in your current database, COPY the database to the new one you just created.
Switch to the new database in phpMyAdmin.
From your notes (or the readme files in your add-ons, remove or update the tables/fields relating to the addons.)
Now, create a FULL CLONE of your shop's folders and files in a sub-directory (can be done quickly and easily in cPanel).
Then, point this "duplicate" shop at the new database by altering the configure.php files as necessary.
Because your software files still have all the addons, this duplicate store is likely to work badly - or not at all, so you must now unpick the php files that relate to unwanted modules.
If any of these files are CORE files, you will need to use a file comparison tool to remove exctra bits of php that these add-ons wrote into the files, and then you will need to determine how to remove or edit the added bits of code.
It's a long process, and is very finicky.... IF all the above is gibberish to you, consider hiring someone to do it for you...