To eliminate any off flavors that may have been absorbed, soak them in warm water for a few hours.
Be sure the stones are covered by at least a couple of inches, so that there's plenty of volume to absorb flavors.
Agitate them every now and again as well.
When you place them back in the freezer, be sure they're dry (any surface moisture will more readily absorb flavors) and keep them in a sealed bag or container.
For what it's worth, it sounds like your sub-par experience is similar to that of many whiskey nerds and my own.
There's really not much need for these things.
You can get a similar amount of chilling by using a thick-bottomed glass placed in the freezer for at least 15 minutes or so.
cooking.stackexchange.com/users/25059/logophobe
If your "whisk(e)y stones" are actually stones, they are pourous all the way through.
You'll need the thouroughly saturate them with water and a bit of vodka to rid yourself of the water- and alcohol-soluble flavors that have been absorbed.
If you don't have the patience for the repeated soakings that will be required, I had good luck putting mine through a self-cleaning cycle in my oven.
You have to make sure that they're completely dried out or they'll crack/explode.
cooking.stackexchange.com/users/27287/Mr. Mascaro
Soapstone whiskey rocks are a thing of the past.
There are much better whiskey stones out there that have a much better cooling power and have no taste.
I love my whiskey, but I love it cool.
I have tried whisky rocks made of soapstone and to tell you the truth, they are terrible.
I have also tried the glass and granite ones and those also do not provide much cooling power.
The stainless steel ones are by far the best I have ever tried, but it is important to make sure they are not just a plated version, also the majority of them are only 3/4 of an inch, but those are still too small to give the desired outcome, the best ones to use are 1 inch cubes.
The best ones I have ever tried are called Great White Ice whiskey stones.
They are 1 inch cubes and are pure stainless steel with a liquid cooling gel in their centers, are smooth and highly polished and they will never scratch anything.
They remain colder way longer
then any other type I have tried, and the best part is, they only have to be frozen from 1-2 hours.
They can also be used in any other type of drink, I also use them in my wine.
They have no taste and they will never break or rust.
Trust me you will never use soapstone whiskey rocks again after trying these!
You can get them on Amazon.
Here is the link [ http://www.amazon.com/Great-White-Ice-Whiskey-Stones/dp/B00CIXQ5C4][1]
cooking.stackexchange.com/users/36591/Jessica
Your experience and other answers are very different from my experience; for me, they work well to temper a wee dram.
:) If they're made of proper soapstone (a common material for whisky stones), you should be in good shape.
If it's something absorbent like limestone or something (which is sometimes used for coasters, and inappropriate for putting in anything)
you've got the wrong substance to start with.
Here's my thoughts, if it's soapstone: Good quality soapstone is essentially non-porous and generally resilient/resistant to staining/smell on its own.
If you think the smell/taste is in the water/ice that has condensed on the outside, give it a quick rinse in cold water after removing from the freezer and before putting in your glass.
This will rinse off the ice crystals and not meaningfully warm the cube.
Soapstone is rather soft (perhaps 4 on the Mohs scale for good quality stuff), and can be polished using conventional methods.
You can scrape and polish off some of the surface with stuff like green scrub pads (e.g., "Scotch Brite"), regular cheap sandpaper, and maybe steel wool or so.
If you think some bits are clinging to the outside, polish them off.
Finish with really fine grit to polish smooth.
Best not to breathe the dust...
This is how I treat my soapstone.
I find that they don't even absorb stuff like bitters.
They work for me, and I like them!
cooking.stackexchange.com/users/25286/hoc_age
Tried soaking my whisky rocks (which I think are soapstone) in lemon juice sealed in a Tupperware container.
Seems to have worked so far.
Gonna dry them out & keep them inside a container in the fridge.
Fingers crossed.
cooking.stackexchange.com/users/38059/Colleen
I made the mistake of buying these  awesome  whisky stones (soapstone) to chill my drinks. Besides the fact that they don't cool the drink down a lot, they acquire a freezer taste and ruin the flavor of the beverage. How can I eliminate this taste? I tried to wash them with soap and water, but I can still taste them.
How to remove the flavor from whisky stones?
cooking.stackexchange.com
<flavor><freezing><cleaning><alcohol><drinks>
cooking.stackexchange.com/questions/48926
cooking.stackexchange.com/users/20668/slybloty
When freezing the stones, make sure they're dry and in a sealed container to prevent absorption of flavours. To clean, soak in warm water or a mix of water and vodka, and rinse quickly in cold water when removing from the freezer to clear condensed water on the surface. Whisky stones should be kept in a sealed container. If they have a smell/taste clean them with water and/or vodka. Rinse any ice off the outside before using them.
Clean whisky stones with water or water and vodka to get rid of the smell. Rinse the ice off the outside to ensure that is not the cause of the smell/taste. Keep whisky stones in a sealed bag or container and make sure they are dry when you put them in the freezer.