It is really hard since MD5 has a good distribution. Your best bet by bruteforcing is adding some hash to your file and appending meaningless data to the end of the binary until the binary has the same hash as the one embedded.
On the other hand if you want to check whether your binary is intact and unmodified you'd be better off by splitting your binary in 3 parts: The part of the binary before the hash, the hash itself and the part after the hash. Concatenate the first and the last part, compute the md5 hash and embed it into the binary.
Like this (example):
foo098f6bcd4621d373cade4e832627b4f6bar
foo | 098f6bcd4621d373cade4e832627b4f6 | bar
md5(foo+bar) = 3858f62230ac3c915f300c664312c63f
foo3858f62230ac3c915f300c664312c63fbar