Again with the questions. After I play I suffer from bad hand aches. Especially in the thumb that supports my flute, and the index finger on my left hand. Is there a way to fix this?

Find some stretches to do after practicing to relax the muscles, and also find some strengthening exercises to do each day to strengthen the muscles you use when you play. If you do both of these every day, the pain should diminish fairly quickly. You can talk to a doctor or physical therapist to get some ideas for the stretches and exercises, or you can find some online--just be careful about the site you use. I have found that many medical schools post basic things like this online.

Check your finger positions and finger postures.

LEFT HAND
I have found many of my students use too much pressure pushing the head joint against their bottom teeth. You only need enough pressure to keep the instrument against the flesh of your bottom lip.

RIGHT HAND
When you are playing is your right thumb bent or buckled? There is no need for it to be buckled or bent backwards. You may want it straight or slightly rounded.

Experiment with how you are holding the instrument.If you feel a spot of tension or spot of pressure see how much less pressure you can get away with. PLaying is not supposed to hurt.

I usually keep it straight, and I've been working on less pressure.

As a former tendinitis sufferer, I absolutely swear by the "Thumbport" by Solexa. It changes the angle of your right hand thumb. For me it means no more aches and pains! They also make a "Fingerport" for the left hand that I have heard is quite good as well but I have yet to try it.

My best advice though would be not to let it get out of hand (no pun intended). Go and see someone - your doctor or good physiotherapist - right away. They can tell you what muscles are involved in the fatige and/or pain. Rest is very important too. Take breaks when playing, even if you don't think you need them. Whatever you do, DO NOT play through the pain! I did and it caused my injury to be worse than it needed to (think scar tissue and recurrence).

Best of luck!

I also have pain in my right thumb and since I also play oboe, the pain has made me to cencentrate on the oboe. I am going to buy the thumbrest from Solexa to se if it works for me.