Well, first I would suggest downloading a stable version of biofat, for reference (download
I'm not familiar with Multimedia Fusion 2 and use WinAPI, as Gemini suggested. WinAPI is simple to utilize, compact/doesn't produce bloated executables, very-well documented at Microsoft websites and compatible with all versions of Windows.
That said, a few pointers and examples:
As henke37 suggested, you'll need to know how the file is handled. Because you stated that you don't know r3000 dis/assembly, I'd suggest looking at the file in hex.
For the EMD archive file, the index (a list of file pointers) is located at the EOF (end of file), like so:
00000000 00000000 000032AC 00003584 00009ABC
The dummy entries (zeroes) represent just that - dummy data - meaning that slot is empty/blank. Judging the list above, it is shown there are 5 files located in an EMD archive, where each value is an absolute pointer to each data.
Obviously, there isn't a 'filesize list', so you'll have to manually calculate the sizes for each file, yourself. Hopefully, I shouldn't have to explain how to accomplish that. ;P
Once you have created your function to handle the EMD filetype, the next step is getting your menu to work, which I will only touch upon. For reference, you'll have to look into something called 'resource' - a simple tool such as 'Resource Hacker' should help.
This is my simple setup for menu IDs, running in the Windows loop (WndProc() function), under the WM_COMMAND message:
szFileName = GetFileName("EMD", "Bio Hazard File (*.EMD)\0*.EMD\0\0");
BIO1_DIS_EMD is the menu ID, located in resource and 'activate' only when the user selects the appropriate option from the menu.
The GetFileName() function is a simple frontend, of sorts, for Microsoft's GetOpenFileName() function that uses a dialog window to select any given name of a file.
Bio1 is a class for the "Bio Hazard / Resident Evil" game, where DisArchive() is the actual function that handles the file (extracts all contents from an EMD archive).
Beyond that, there's not much else that I can help you with, as I haven't the time to teach programming skills. I hope that helps.
Create a Win32 project and you have exactly what you need to develop a BioFAT clone.
Ironic, because the classes I've created are part of something of a whole, which I call "BioClone".