No, the software is not updated to work with Windows 8.1 64bit. I have checked the official website and these are the supported operating systems for version 2.0:
Windows® XP Home (SP 3+), Professional (SP 3+), & Professional x64 (SP 2+). Windows Server® 2003 R2, Standard (SP 2+) & 2003 R2, Standard x64 Edition (SP 2+). Windows Vista® Home Basic, Home Premium, Business, Enterprise, & Ultimate (32/64-bit) (SP 1+). Windows Server® 2008 Standard (32/64-bit) & 2008 R2 Standard (64-bit). Windows® 7 Home Premium, Professional, Enterprise, & Ultimate (32/64-bit). *ScandAll PRO runs as a 32 bit application and requires Microsoft.NET Framework 2.0 SP2 or later.
As you can see, there is no Windows 8.1 compatibility present or mentioned in this list.
Official website: http://www.fujitsu.com/us/products/computing/peripheral/scanners/software/scandall/