Dipstick covered in oil-help!

[DaveG]

So, I just did my 10000 mile oil change on my 2010 liftback. Its the first oil change for this car I've done, since the dealer gave me 1 free oil change for 5000 miles. I've changed oil before. I looked up in the owner's manual that the Yaris uses 3.9 quarts of oil, so I put in 3.5, thinking that I'd see it on the dipstick, and then put in just a little more. Well, when I pulled out the dipstick, it was covered in oil about halfway up. Not the oil level part with the two dots, but halfway up the entire dipstick!
So, is there something I'm doing wrong, or did I put way too much oil in the car? It looked like this after running the engine for 1 minute, and also after running for 5 minutes and cooling for 5 minutes. Is the car safe to drive for a while? And, if I put too much oil in, how do I get it out???
Thanks in advance for the help!
Dave