How should I have handled the turn raise? Should I have look to get it all in there after the raise? Also as played should I have bet the river? I feel I lost out on an opportunity to get some value somewhere but not sure how best to play this scenario.

PokerStars No-Limit Hold'em, $0.50 BB (9 handed) from (Format: FlopTurnRiver)

Button ($184.85)
SB ($47.65)
BB ($122.15)
Hero ($88.70)
UTG+1 ($71.45)
MP1 ($42.30)
MP2 ($31.15)
MP3 ($44.25)
CO ($38.25)

Preflop: Hero is UTG with Q, K.
Hero calls $0.50, UTG+1 calls $0.50, MP1 calls $0.50, 3 folds, Button calls $0.50, SB completes, BB checks.

Flop: ($3) 9, 8, 3 (6 players)
SB checks, BB checks, Hero bets $2, UTG+1 calls $2, MP1 calls $2, Button calls $2, SB folds, BB calls $2.

Turn: ($13) 6 (5 players)
BB checks, Hero bets $8, UTG+1 folds, MP1 raises to $16, Button folds, BB folds, Hero calls $8.

River: ($45) Q (2 players)
Hero checks, MP1 checks.

Final Pot: $45

Whether you should shove the turn or not depends on the opponent - he had $40 to start the hand and after he minimum-raises to $16 he has half his stack in the pot - At these stakes with no read on villain, I would 3-bet turn all-in.

However, since you just called, why check the river? Are you hoping he min-raised you with the A[s]-x and now he'll bluff on the river? No reason to not lead the river all-in as played.

You have the best hand like 97% of the time here, try to get all the money in.

Well guys,

As it turnend out I won while MP1 had a set of 3s. But I think my problem developed from the start. I was almost certain that once I bet out on the flop and got multiple calls, there was at least one other flush draw out there w/ me. So how can I play for my stack if I am not holding the As? Am I wrong in my thinking?

You don't need the nuts to stack off for crying out loud. Shovel money in there. He minimum raised so he likes his hand, reraise him right now! 2nd nuts is plenty, you'll be shown sets and lower flushes a big bunch of the time.

Also as played you let him see if he could boat up and clobber you for free: you're going to have a tough time folding to a push even if the board pairs.

The only time I worry about stacking off with the 2nd nuts is when it's a one-card hand, i.e. [Qs] on a board of [9s][2s][4s][7d].