Come up with an overall idea for your character: his name, his superpower and his general personality. It doesn't need to be too detailed at this point--just a sense of who he is and a hook to make him stand out from other superheroes.
Develop a background, origin story and modus operandi for your hero. Decide who he was before he gained his powers and what drove him to use them for the betterment of society. Cover the means by which he gained his power in significant detail, and be sure to give it a sense of internal logic (he wouldn't gain heat-generating abilities if he were frozen in a lab accident, for example). In the Marvel Universe, many (though not all) superheroes are simply born with their powers, which makes them hated and feared by the remainder of the population. If you go that route, it will have considerable bearing on his history and personality.
Figure out a costume for your superhero, as well as his overall look. The costume should evoke his powers in some logical manner, either through the color, the logo or similar details. In some cases, the costume is the power--like Marvel's Iron Man, for example, who basically just built a high-tech suit. In addition, think about what your hero looks like physically--including height, weight and facial features--and incorporate that into his overall image. If you like to draw, then draw your own picture of your superhero. If not, you can use an automatic costume generator like HeroMachine (see Resources).
Consider any problems or difficulties your hero's abilities may cause. Marvel Universe characters often find their powers to be a double-edged sword, interfering with their personal lives, creating new difficulties and challenging their ability to be happy in ways they never expected. There should also be at least a few weaknesses or vulnerabilities present: situations in which your hero's abilities are useless, and may even constitute a drawback.
Determine where your superhero lives. Most Marvel characters operate out of New York City. If your hero lives there, he might run into some of the others from time to time. Other cities have fewer Marvel characters, and one of them may be a good place for your hero to "come into his own." Outer space makes an interesting locale, too, provided it fits your character's background. Alien species like the K'ree and the Skrulls dwell out among the stars, as do adversaries such as Galactus. Where your hero is based has an effect on the kind of people he meets and the adventures he has.
Build up any sidekicks, girlfriends, parents and similar supporting cast members to fill out your hero's stories. Decide how they are affected by your hero's adventures, whether they know who he truly is, and the ways in which he interacts with them--both while he's wearing his costume and when he's just a "normal person." While at least some of these characters should be totally original creations, sprinkle a few existing Marvel characters into the mix as well. Maybe your hero grew up in Professor Xavier's School for Gifted Youngsters or teams up with Daredevil to fight street crime every now and again.
Pick some villains for your hero to fight. Choose from an assortment of Marvel villains, such as Magneto or the Kingpin, who seem to fit in with your hero's background. Add at least one or two original villains of your own, to help make your character distinct. Don't just determine who he has fought, but why he fought them and the circumstances that brought them into conflict. A hero is only as good as his villains; luckily, the Marvel Universe has some of the very best.