Are you saying that the keyboard is split? If it is then what you'll probably want to do is determine which channel the left-hand notes are being sent on, and use those notes. In many cases the right-hand zone will be on channel 0, and possibly also on channel 1 (if the right-hand zone is using a dual or layered sound), with the left-hand zone being on channel 2-- but that isn't always the case, so it's best to use a MIDI monitor to see which channels are being used for what. And yes, it's possible for the two sides of a split keyboard to overlap if either side has an octave shift applied to it.
If the keyboard is not split, and what you mean is that the right and left hands are moving all over the keyboard (as is typical when playing the piano), then I guess what you're asking is how to identify the notes being played by the left hand versus the right hand, and not necessarily which notes are the "bass clef" notes. If that's the case, then I'm not sure whether there's a simple solution, since there's really no way to be certain which notes are being played by the left hand-- for instance, a piano piece may require that the pianist play a lengthy series of ascending notes by starting with the left hand, then switching to the right hand, then reaching over the right hand to continue with the left hand, then using the right hand again, etc.
If it's safe to assume that the left hand will always being playing to the left of the right hand, then you might be able to figure out which notes are being played by which hand based on how close together or far apart they are, where it's assumed that the close-together notes are being played by one hand and the largest gap is assumed to separate the left-hand notes from the right-hand notes, but that won't always be true. So I doubt there's a 100% fool-proof "automatic" method that could be programmed on a computer, although you might be able to do it manually by eye-balling the notes of the song in a piano roll editor and making your best educated guess.