MB does not target script files. That means MB will not target; JS, JSE, PY, .HTML, HTA, VBS, VBE, .CLASS, SWF, SQL, BAT, CMD, PDF, PHP, WSF, etc.
It also does not target document files such as; PDF, DOC, DOCx, DOCm, XLS, XLSx, PPT, PPS, ODF, RTF, etc.
It also does not target media files; MP3, WMV, JPG, GIF, etc.
Until MBAM, v1.75, MBAM could not access files in archives but with v1.75 came that ability so it can unarchive a Java Jar (which is a PKZip file) but it won't target the .CLASS files within. Same goes with CHM files (which is a PKZip file) but it doesn't target the HTML files within. MBAM v1.75 specifically will deal with; ZIP, RAR, 7z, CAB and MSI for archives. And self-Extracting; ZIP, 7z, RAR and NSIS executables (aka; SFX files).
MB specifically targets binaries that start with the first two characters being; MZ
They can be; EXE, CPL, SYS, DLL, SCR and OCX. Any of these files types can be renamed to be anything such as; TXT, JPG, CMD and BAT and they will still be targeted just as long as the binary starts with 'MZ'.
MB targets mainly non-viral malware. The exception being a virus dropper ( a malware file that drops a virus and starts a virus infection but is not infected with the virus ) and worms ( such as Internet worms and AutoRun worms ).
MB is incapable of removing malicious code that has been prepended, appended or cavity injected into a legitimate file. That means if a file infecting virus infects a legitimate file MBAM will be unable to remove the malicious code. An anti virus application should be able to remove malicious code from an infected file and hopefully bring it back to its preinfected state. Which may or may not return the file to its original, non infected, checksum value.
A file infecting virus will prepend, append or cavity inject malicious code into a legitimate file. Once infected, that infected file can further the infection by infecting other legitimate files.
On the other hand there are trojans that will prepend, append or cavity inject malicious code into a legitimate file. However that file can not infect other files. The infection stops with that targeted file. These files are either deemed to be "trojanized" or "patched". Since MB can not remove the added malicious code, at best MB will try to replace the trojanized file with a legitimate, unaltered, file.
MB is not a historical anti malware solution. That means it will not target old malware. It's intent is to target 0-Day malware. Malware that is infecting computers Today with malware found in-the-wild, Today. That means that something like the BugBear which infected years ago will not be targeted by MB. Malwarebytes will actually cull their signature database for malware that is no longer seen in-the-wild Today. This is why Malwarebytes requests samples that are submitted for detection consideration be no older than 3 months old.