I have been trying to extract Models and Textures from this game, i have Quickbms and the gi_joe_cobra.bms but it's not .BIN files but .BIN_BE files and i don't know what to do here, any help?

These are the formats i have found in the gamefiles:

The BIN(meaning most likely the Models and Textures) files are in .BIN_BE
The Levels files are in .GBR_9_BE
The Sound files are in .PLL
The Lipsync data is in .PAK_BE

All the Animation files are in one .ASB_61 file

The game was made by Double Helix Games who also made Silent Hill: Homecoming (2008) and this game came out one year later.

the BE will be most probably Big Endian. Try to set it in bms. And also post the samples.