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I'm trying to find the best application on windows to do this HD to SD conversion for a video server which requires files to be exactly 720x480/29.97fps MP4 H.264 to function. I can't find any options for leterboxing in Handbrake so I suppose I'll need an alternative.

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You can use ffmpeg, a free command-line tool, to do this:

Without letterboxing, NTSC wide pixel-aspect

ffmpeg -i input.mp4 -vf "scale=720x480,setdar=16/9" -r 30000/1001 -c:v libx264 -crf 20 -c:a aac -movflags +faststart output.mp4 

With letterboxing, NTSC 4:3 pixel-aspect

ffmpeg -i input.mp4 -vf "pad=1920:1440:0:180,scale=720x480,setdar=4/3" -r 30000/1001 -c:v libx264 -crf 20 -c:a aac -movflags +faststart output.mp4

With letterboxing, square pixels

ffmpeg -i input.mp4 -vf "scale=720x404,pad=720:480:0:38,setsar=1" -r 30000/1001 -c:v libx264 -crf 20 -c:a aac -movflags +faststart output.mp4

Read up on sample or pixel aspect ratios, if you're unfamiliar with them. Your requirements make it sound like NTSC-spec files are expected, so try the commands in the order listed.

If your source audio is MP4-ready i.e. of codec AAC or MP3, then you can replace -c:a aac with -c:a copy

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