Debbie Ducommun has some great suggestions for rat restraint in her Rat Health Care booklet - it's cheap and worth every penny. But perhaps you haven't ordered that yet so I'll tell you what we do:
First and foremost you must be confident. Rats sense your nervousness and they tend to be behavioral nightmares if you're not confident. I'm not suggesting you squeeze your rat silly and shatter his bones, but you must be firm.
Grounding: Grounding is most important. Your rat does not like flailing around. If you can give him some footing he'll be most appreciative.
Security: Hold your rat securely by holding him by the nape of his neck. His mom did it and you can too.
I find that the best way you can do anything is with two people. This way one person can hold the rat in her arms securely and provide distractions while the other adminsters a shot, gives oral medications, drains an abscess, trims teeth, etc.
Barring the two-people approach, I find that letting the rat run around to expend some energy, then, when exhausted, holding
the rat by the nape of his neck is the next best approach:
Some activities aren't conducive to rats lying flat. Perhaps there are more, but the only one I can think of is teeth
trimming. This definitely takes two people. The person holding the rat should hold him similar to what is depicted below.
Of course in the case of trimming teeth, you would not use your index finger to pull the neck skin downward to raise the
head upward as is pictured. Instead, you would use your index finger to pull the cheek-skin backwards in order to expose the
teeth. This way the second person can focus on safely getting into the rat's mouth.
I would also recommend that the person holding the rat use their other hand to hold the rat's feet. Although there is no
harm in dangling the rat in the manner pictured, your rat would prefer having a place to put his feet:
