Atomos Samurai and Ninja footage

We need additional information before you can get a straight answer.  The major one being the video codec of your footage.  It also wouldn't hurt to answer the questions you'll find on the following page:

http://forums.adobe.com/thread/961743

Samurai? Is this footagae coming from a video game? If so, you'll need to change the capture settings to a more AE-friendly codec.

AE is a compsiting systme, not a video editor. Because everything AE does is based on absolutely every pixel in every frame, After Effects prefers full-frame codecs that have no temporal compression and not based on long group of pictures quantization.

The Atomos Samurai is a device that records signal from a camera to ProRes (or sometimes Avid DNxHD). If After Effects is telling you that it can't import the file, the most likely reason is that you don't have the ProRes decoder installed on the computer.

We have tried SD and HD footage 220mega bits per second to "replace with AfterEffects Comp" from with  but when Ae opens it is just color bars and no footage. What am I doing wrong I have also tried to import directly to Ae but it says can't import file file might not be supported. Is this becuase it is a MOV?

This is a known issue. I read a tech note on it somewhere. Obviously the ProRes it creates is not the same as in FCP and thus AE cannot handle it. you will have to conform/ convert it first.

Mylenium

Try importing the same footage into Premiere Pro. Make sure that you've applied the recent updates (choose Help > Updates). If this is the same issue that I know about, we have fixed it in a Premiere Pro update but not an After Effects update.

Ah, OK. Then it probably is the bug that I'm thinking of. Yes, you just need to transcode to a different format if you're going to use this asset in After Effects.