I am about to apply for a security clearance through my company. My father wants me to travel with him to our home country in the Middle East. I am worried that this might result in my application being rejected. I have seen example applications online where the applicant was asked about any contact he had with his home country in the Middle East, so visiting the country seems to be even more problematic.
It might depend on which country. I had visited the middle east before getting my security clearance several years ago and it didn't harm me, but the training materials identified certain countries as more likely to cause red flags. It might also depend on whether you are a national of that country or have family ties there.
Fortunately, you don't have to guess. If you're getting a security clearance in order to do your job, then your employer has, or has access to, a security officer whose job includes answering questions like this. If you don't know who that is, the person who asked you to apply for the clearance should be able to tell you. You might also find answers about this on the web site of whichever government agency is issuing your clearance, or in the application bundle.
When you apply for the clearance you'll have to identify all foreign travel (countries and travel dates) for some period of time (last ten years? something like that). Once you have a clearance, you'll need to notify your security officer before you begin any foreign travel. If your intended destination is a problem, you'll hear about it before it jeopardizes your status.