It is said that it is regarded as a best practice to name child Muhammad (name), but in western countries where first name is on your passport e.g Muhammad Ajmal Khan, whereas Ajmal is real first name but as on ID card or passport will make Muhammad name first, is it ok to leave Muhammad name out of name to end this confusion? Or is there anything like prefix that you mention on birth certificate? Today I had a baby boy and I am confused over naming convention.
Who said he has to be named Muhammed? You can name him anything, but it has to be a good name that doesn't represent anything bad. And having a prefix isn't necessary, it is rather a culture. And the best names are the names which start with Abdul (e.g Abdullah, Abdul Rahman, Abdul Latif, Abdul Aziz etc.)
Read this http://www.islamcan.com/names/names-that-are-preferred-and-that-are-undesirable..shtml#.VlagUnOwrqA It talks about this matter in detail.