Extracting usable h264 from .mkv?

[aNToK]

There's probably a simple solution for this but I can't seem to find it.

I ripped several Blue-ray disks to filter and recode for my collection, filtered them with MCTemporaldenoise, and used Megui to compress them with h.264/avc and merged them into an mkv file.

After viewing them, there's a few tweaks I want to make, but using MKVExtract or any other method leaves me with a video file with the .h264 extension that nothing seems to want to read.

I've worked around it with the mkv plugin for VDub to resave it as an avi file but is there a more direct way to do this?

Is there a plugin or filter to allow me to use the h264 extension in my avisynth scripts or is it some kind of container issue? I'm a bit lost...