A man with the same name as his father uses “Jr.” after his name as long as his father is alive. His father may use the suffix “Sr.” for “senior.” The son may either drop the suffix after his father's death or, if he prefers, retain it so that he won't be confused with his late father.
What is considered a suffix in a name?
The suffix is an explanation of the first name, not the last. "John Doe Jr." means he is John, the son of John. In a full name listing, the suffix follows the last name because the person is primarily known by is given name and surname, the suffix being a secondary piece of information.
Is father a last name?
The father's name is not considered a middle name. Instead, it is considered a last name. The same is true for females; they do not take their husband's last name. They go independently by their given name, followed by their father's name, and then their grandfather's name, even after marriage.