Not quite, because they were not all direct clones the way we think of cloning in real life, because in the Metal Gear universe, they could do "selective cloning".

I forgot the details of how exactly they described it (and I haven't played beyond MGS3 yet). But in MGS, Liquid and Solid have a conversation about it, where Liquid insinuates that they took the "best genes" of Big Boss to clone Solid (who actually looks like Big Boss), and used the remaining "weak genes" to clone Liquid. I would bet that this whole explanation is also sprinkled with a bit of nanomachines-related lore in the later games.

Also, their differences in looks could be explained by environmental factors and style choices. I would argue that Solidus looks just like Big Boss and Solid, but aged, more muscular, and with different facial hair.