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I have recently purchased a bottle of Balvenie 12yo double wood.
As I removed the cork from the bottle small bits of cork crumbled off and fell into the whisky.
These bits are very small but noticeable. Will these cork bits have an effect on the nose and taste of the whisky? Or is the only annoyance of these bits that they are visible inside the bottle.
@Fabario
If you look under "About Whisky" in the vlog tab, there is a nine minute video given by @horst_s discussing how to remove cork from a bottle.
In short, you might want to pour your 12 year into another bottle, clean the original and the pour it back in. Pour slowly and make sure you use a coffee filter so the cork doesn't leak into the new bottle.
@Fabario
Hm. This is a tough one i reckon. To remove cork you would have to oxygenate the whisky quite a bit. Im not sure if the cork would leave more taste or the added oxygen to the whisky.
If you want to remove the cork, you can run it through a filter.
Btw a very fine dram you've bought!
I would chose to filter it out, if it leaves you annoyed every time you have a dram.
Slainté
http://www.maanedensmalt.dk 
@Fabario
In my experience, these small bits of cork tend to float. If you don't want to go to the trouble of pouring the whisky through a filter, I have had good luck removing floating cork particles with a cotton swab. The particles will stick to the swab and can then be removed. A swab is also good for removing particles adhering to the inside of the bottle above the whisky.
I don't worry if I can't get out every last particle. A few tiny pieces of cork won't hurt you.
@Carlton
Good idea.