Please begin with the overview of the service at http://www.windowsazure.com/en-us/develop/media-services/, get familiar with how to upload assets and create encode jobs. In your case, you would need to download the sample code, build and run it.
Then, for trimming, you would submit jobs where the preset to the Windows Azure Media Encoder would specify your time interval as a , for example:
<Sources>
<Source
AudioStreamIndex="0">
<Clips>
<Clip
StartTime="00:00:00"
EndTime="00:00:09.9740000" />
</Clips>
<CaptionFiles />
</Source>
</Sources>
I can explain further details for exactly how to build the presets, but please also confirm that you know the exact in and out points you want to trim, in time format (HH:MM:SS.MMM)?