How do I free up space on my MacBook Pro despite using an external drive and CleanMyMac?

Follow these instructions to free up storage space:

Free up storage space on Mac - Apple Support

Uninstall third party apps that claim to clean, manage, etc. CleanMyMac is one such app.

You can also use a 3rd party disk inventory tool like OmniDiskSweeper (free), Disk Inventory X (free) or DaisyDisk (paid) to get a graphical and/or heirarchical view of your largest files/file types including those in the Library folders.

from:

How to free up ‘System Data’ and other st… - Apple Community

NB> those utilities only IDENTIFY big Files, they do not remove them -- despite names like OmniDisk Sweeper, it does not sweep files away, only makes a sweep of your drive(s) to identify large files.

The categories shown are extremely broad classes of things, and can not be directly correlated to items such as the /Applications folder. You are taking those classes too literally.

If you have enabled Time Machine, but failed to attach your external drive in a timely fashion, you could have collected a large backlog of Time Machine snapshots: lists of files waiting to be written to your external drive.

if that is the case, connect your external drive and allow Time Machine to make its next incremental backup to the external drive.

if that does not solve the problem, you will need to determine the top handful of large files that are clogging your Mac. That can be dome with Finder, or with a third party Utility.

There are two schools of thought when it comes to dealing with CleanMyMac aka BrickMyMac

CleanMyMac , aka “ BrickMyMac “

The steps in #1 below is predicated on the Offending  Application has been Removed as per the Developers Specific Instruction 

# 1 Some Contributors suggest restarting in Recovery Mode and choosing to Reinstall the Operating System over the existing installation. 

This may or may not replace elements of the  Home Folder ( User Account )  and replace any corrupted or removed elements and make things right.

#2 - Then there are Other Contributors ( like myself ) would suggest  from this link Use Disk Utility to erase a Mac with Apple silicon.

For Intel computer >> Use Disk Utility to erase an Intel-based Mac followed by How to reinstall macOS

Thereafter to start from scratch and install all Required Applications directly from the Apple Apps Store or Directly from the Developer.

If going this route - I suggest Not using Startup Assist to migrate things back as this will probably Re-Introduce the existing  issue at the time TM Backup was made 

<< Can you explain why Cleanmymac is bad / should be removed? >>

Your extremely well-crafted Mac does not accumulate random filth that can benefit from any third-party software to help remove it.

Caches are created to speed up your Mac. Caches hold temporary items that might be needed again soon, so that those items do not need to be fetched again, causing delays. Emptying caches SLOWS your Mac, but if you wish to remove caches, the Best Practice is to do a Restart, not run a third-party app.

CleanMy Mac has no special knowledge of what should be removed in removing apps. It has been known to attempt to remove vital parts of MacOS itself, assuming they were part of a package, and fails to respect shared items that are in use by apps in addition to the app you are trying to remove. It just guesses.

CleanMyMac has been implicated in cases where it was invoked and the Mac it was running on was so damaged by it, that a complete MacOS re-install was required afterward. CleanMyMac has such a bad reputation here that senior contributors refer to it as "BrickMyMac". CleanMyMac is not just useless, it has proved itself dangerous.

There is an application called DaisyDisk that is available from the vendor site, or the App Store. MacWorld did a review of it back in September 2024. My understanding is that, instead of promising to magically free a lot of space – then removing system files that are better left alone – it helps you to understand which files take up the most space.

Note: I'm not a user of DaisyDisk, or associated with the developers. I've just heard of it.

What are the names and sizes of the five largest files still on your Mac?

(be sure to run as an ADMIN user)

What Utility are you using to find them ?

Once you have exhausted what Finder can see, any of the third-party Utilities would be better for making additional progress, provided you use an Admin user (that has the right to see almost everything.)

This is because Finder does not look in hidden system directories.