How do I clear system storage from my MacBook Pro?

When you deleted GoodNotes, the space it used didn’t vanish, it got moved under “System Data” temporarily, likely due to snapshots, caches, or local Time Machine backups. That’s why your system data ballooned.

To clean it up, disable Time Machine (if it’s on), restart your Mac, and run tmutil listlocalsnapshots / in Terminal to see any local snapshots. Delete them with sudo tmutil deletelocalsnapshots <date>. Also, use a tool like DaisyDisk or GrandPerspective to visually map large hidden files. But don’t obsess over “System Data” too much—it fluctuates and macOS handles most of it in the background.

You can also clear temporary files and caches from ~/Library/Caches

Only if the System Data is still bloated after this should you look at Time Machine snapshots, which often hide in the background and bulk up the “System” storage. You can inspect them with tmutil listlocalsnapshots /

I would ignore that because this system data will make room when you need more space on your Mac. These are some cache and temporary files that will be erased by the system whenever you try to save more files.

Extracted from the Apple Article (Settings > General > Storage [Scroll Down] See the Pic above:

"System Data: Contains files that don’t fall into the categories listed here. This category primarily includes files and data used by the system, such as log files, caches, VM files, and other runtime system resources. Also included are temporary files, fonts, app support files, and plug-ins. You can’t manage the contents of this category. The contents are managed by macOS, and the category varies in size depending on the current state of your Mac. You can manage your data that falls outside the other categories using the Finder or the third-party apps that created it."

You can clear system storage on your MacBook by restarting it and then emptying the trash. If you still need more space, you can also try deleting large files or unused applications.