You'll need to use "coin control"... Use the "view -> show coins" menu option... Then click on the "coins" tab.
Then select a couple of hundred of the small value "coins" displayed, right click and select spend.
This will allow you to then consolidate all the selected coins into a single output of greater value. Repeat for as many times (selecting hundreds of small value coins) as necessary until you only have a couple of "large value" coins left.
That should enable you to then conduct one transaction that contains all your balance.
Note that EVERY transaction you create will require a fee... And as fees are based on the amount of data being included in a transaction, the consolidation transactions could get quite costly if you have a lot of inputs that are less than 1000 sats (0.00001000 btc).
I suggest you read LoyceV's very good post on output consolidation here:
https://bitcointalk.org/index.php?topic=2848987.0