The 64-bit version of Agnitum Outpost Suite adds only 64-bit right click menu entries, so you cannot scan files from inside a 32-bit file manager. I was using XYPlorer previously and had to switch to Windows Explorer whenever I needed to scan a new download, so I found a way to add the 32-bit context menu entry without editing the registry. You may find this useful if you use Agnitum. I haven't tried this with other security programs.
To add the right click option, Agnitum Outpost Suite registers a .dll file, op_shell.dll. You need the 32-bit version of this .dll file. I installed the 32-bit version of Agnitum on a virtual machine and copied the .dll file over to my Vista x64. Just place the 32-bit version of op_shell.dll in C:\Windows\syswow64 and register it. Now, you will see the right click option "Scan for Malware" in FreeCommander.
Agnitum Outpost Suite context menu entry on Win x64
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