I am a seafarer (marine engineer) and I have to often visit different countries. This time I received my sign-off from Iran and they stamped my passport. Would this cause a problem for getting a US C1D1 visa since my next company wants me to have this visa? I am an indian national.
The US does not usually discriminate against people who have visited any particular countries. They may ask questions on entry about what you were doing there, for example, but as long as you can answer them honestly and there's no issue with what you were doing (weren't building nuclear reactors were you? ;)), you should be fine.
When you apply for a US visa there are some questions about what you were doing, whether you're a member of certain groups and the like. But as long as your application doesn't raise flags, you should be OK.
Thinking of people I know - I have a friend who has been to North Korea and then the States, without problem, same process, as long as your application has no red flags, it will be processed. Another friend IS Iranian, has been back several times while studying and visiting Chicago as well, again, no problems getting visas.
Saying that, the one factor it can come down to is the border guy on the day you enter. But stay calm, be open and honest, and it should be fine. After all, if your visa has been approved, by that stage it should be easy.
Go ahead and apply, worst case they do raise a problem and then you can deal with it. But for now, I'm pretty sure you haven nothing to be concerned about.