intake studs

I am cleaning up the heads to install the intake today and after stripping off the silicone I see two small studs in the center of the valley at each end. Were these used to set the intake correctly in the factory? The intake I took was a LD4B and I could see the studs had dug into the underside of the intake. That doesn't seem right. What do you guy's do? remove them or knock them down further.
Thanks
AL