Hi,
The readme file contains more examples of how to use fciv.exe, including using different algorithms and generating hash values for entire tree folders.
In the link your provided to the tools it states: "Warning The Microsoft File Checksum Integrity Verifier (FCIV) utility is an unsupported command-line utility that computes MD5 or SHA1 cryptographic hashes for files. Microsoft does not provide support for this utility. Use this utility at your own risk. Microsoft Product Support Services (PSS) cannot answer questions about the File Checksum Integrity Verifier utility."
Try reposting your question(s) to TechNet Forumfor IT Professional assistance.
How to Use Article on the utility
http://www.computerweekly.com/tip/How-to-use-the-Microsoft-FCIV-command-line-checksum-tool
Good Luck!