ok so you change your directory issue a system command and you want the output to go somewhere other than the current directory?

I see two options

1. if your build program has a command line option where you can change the name of the output directory you can use the Cwd module to capture the name of the starting directory and save it in a varible, then use that as a parameter to build. I don't know of "build" so i can't say if this is possible.
2. If you know what the name of the output file will be use File::Copy to send that output file wherever you want after it has been created.