The scene I am thinking of is in Isengard when Saruman is ordering the forest to be burned. The forest is on the edge of the mountain.
Fangorn Forest and Nen Hithoel
Lake Te AnauThe Mavora Lakes was the location for Fangorn Forest and Nen Hithoel. The lakes are situated off the Te Anau Highway pass Mossburn or you can take an unpaved road near Te Anau which takes about 45 minutes by car. Just before the turn off to Mavora Lakes, you will see the Fangorn Forest to your left. The township of Te Anau is the gateway to to the spectacular Fiordland National Park.
An independent confirmation:
Fangorn Forest edge:
Aragorn, Legolas and Gimli follow Merry and Pippin's trail from the mound of burnt orc bodies left by Eomer's Riders of Rohan.
In addition, Isengard itself was filmed here:
Isengard Gardens and the Orc Tree
Harcourt Park on the Akatarawa Road in Upper Hutt about 20 minutes from Wellington City was the location for Isengard Gardens and the Orc Tree. The Akatarawa Road cuts through the Rimutaka Mountains.
One more bonus location:
Fords of Isen
Lake Pukaki Kaitoke Regional Park was the location for Rivendale and the Fords of Isen. Kaitoke is north of Upper Hutt near Wellington. The park is sign posted on SH2 and offers BBQ areas. The position of Rivendale is sign posted at the entrance of the park. You can see the Fords of Isen from a bridge near the car park.
To add to DVK's answer, they also produced an artificial forest within the studio, complete with real leaves, soil, rocks, some trees (I forget if they were all artificial) and even the occasional insect (the Weta) that followed the leaves. They often contructed a back up studio version for real locations in case of elements out of their control.
My source for this is the Appendices of the LoTR Movies. I would recommend watching these if you are interested in the making of the series.