Yes...I recommend you do so.
For comprehensive cleaning (disinfection), especially on computers with multiple active user accounts, its recommended to do a THREAT SCAN on each user account
so everyone's registry gets scanned. Although Malwarebytes scans other user's folders, it is best to run a separate scan under each user profile
to ensure detection and removal of any remnants/orphan registry entries which may have gone undetected during the initial scan. Malwarebytes Anti-Malware stores each configuration in the current user's key so each user can configure it to operate differently. This may have changed with v2.0 but I have not come across any updated information which indicates otherwise.
Note: Most anti-virus and anti-malware scanners will scan all files on each drive you configure the program to scan if the program is run while logged in with an Administrator Account
to include all user account files in the Documents and Settings folder, and User AppData folder. However, not all anti-malware scanners work the same way and some may not look at other account user's registry entries. If malicious files are removed during a scan, the infection can be disabled but orphan (leftover) registry entries related to the malware may remain and require separate scanning for each account in order to completely remove them. You should always read the scanner's documentation and help files to determine the vendor's recommendations, then check the program's configuration settings to see what is being scanned.