Is it good practice to rebuild index on FileTable?
(converting my comment to answer)

FileTable uses Filestream technology. From Paul Randal's blog - Defrag the NTFS volume if needed before setting up FILESTREAM, and periodically to maintain good scan performance. 

Instead of rebuilding, you should defrag the ntfs volume as suggested. 

Also, highly suggest to read - Best Practices on FILESTREAM implementations - by Pedro Lopes (Senior PM at Microsoft Database Systems)