First thing first. You cannot travel to Bhutan on your own. As a tourist you can only come to Bhutan through international or local travel agencies. You might want to know why, but to cut the long story short it is the government’s  policy to take in limited number of tourists.

So you must follow simple steps to get your tour planned:

Choose your tour plan (discuss with your travel agent making customized and best tour plans)
Register with a travel agent and send your details (passport copies)
Pay the total amount of money for planned tour in advance (yes, before you come to Bhutan) to your travel agency. It must be paid in US Dollars.
After receiving your money, your travel agency will process your visa (which is not difficult to get once you have paid).
After getting the visa, you can fly in to Bhutan and relish the wonderful vacation.