Hi Nikola,
Thank you for your question.
In Unix, and I think MinGW too, you should be able to build fuzzylite in 64bit passing the option -m64 to the compiler. However, most likely you will have to remove the -Werror flag as there are some warnings being raised when returning std::vector::size_t as an int from some methods. The -Werror flag converts warnings to errors. Let me know if this helps.