You need to pass the FibonacciElement directory as the parameter to your VM Translator.
Your VM translator should write the bootstrap and process all the VM files in the directory to directory-name.asm.
Here's my translator running on FibonacciElement
[D:/TECS/projects/08/FunctionCalls]
% hvm3 -o0 FibonacciElement
Hack VM Translator 3.1.7
Output to file FibonacciElement\FibonacciElement.asm
Processing directory FibonacciElement
Analyzing FibonacciElement\Main.vm
Analyzing FibonacciElement\Sys.vm
2 Functions, 0 unused.
Processing FibonacciElement\Main.vm
Processing FibonacciElement\Sys.vm
[D:/TECS/projects/08/FunctionCalls]
(The "analyzing: steps are creating a call graph to enable removing uncalled functions. Removing them can greatly decrease the size of programs that us the OS VM files.)
--Mark