Is it possible to convert mkv file to 1280x720 QuickTime or other file without quality loss? I need some format that After Effects can handle and QT with animation/jpg/png codec would be the best option.
You will first need to extract the video from the .mkv file. Use MKVExtract GUI. Afterward remux it wiht MP4Box into a .mp4 file which Quicktime will be able to handle. YAMB is a GUI for MP4Box.