Need to buy at least four grapeshot bombs... The tunnels are basically small holes rounded by bones locatedon the surface of the forest. If you search well you will find all of them really fast...As you approach them you will be prompt to destroy them... No need to throw the bombs... Good luck :)

First you need to gain enough knowledge about Nekkers. When it is 2 out of 3, there will be an entry in your Character screen that mentions that Grapeshot bomb (or perhaps it is your quest entry in your Journal) can be used to destroy the Nekker tunnels.

You can buy the bombs and the crafting diagram for the bombs from Cedric.

Thanks guys