usr folder randomly appeared on my hard drive in finder. Is this malware? Virus? How do I delete it and protect my computer?

The appearance of the usr folder with aliases like X11 and X11R6 on your Mac’s root directory might look suspicious at first, but it's likely not malicious. These folders are typically part of the Unix-based structure of macOS and are essential for system operations, especially for applications that rely on UNIX or X11 components.

In macOS, the /usr directory is normally hidden, but sometimes after an update or certain applications’ installations, these system directories become more visible temporarily. macOS Sequoia may have adjusted how certain directories are managed or displayed.

FYI. The X11 and X11R6 aliases are related to XQuartz, an implementation of the X Window System for macOS, which some applications (especially cross-platform ones) rely on. Even if you didn’t install XQuartz manually, other applications (like Logic Pro) or system updates could have placed these aliases here to maintain compatibility.

However, if you still feel uneasy, running a full malware scan with a reputable tool like Malwarebytes or monitoring system behavior through Activity Monitor can help confirm that everything is secure.

You're very welcome!