Firefly is completely command driven, meaning that it has no graphical user interface. All commands describing the molecule and what computations to perform must be stored in an input file. The input file must be placed in any directory you like, provided that the .bat file contains the full path to the file. If your .bat file contains the input file name, but not the full path, then your input should be in the same directory where the .bat file is present. The directory where you run the .bat file must have access to the firefly executable and extensions (the .ex files). This can be achieved in two ways: either place the program and extensions in the directory, or else modify the PATH system variable to include the directory where you do have Firefly.