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Everything posted on Miguel Guhlin’s blogs/wikis are his personal opinion and do not necessarily represent the views of his employer(s) or its clients. Read Full Disclosure
More tutorials for VLC Media Player here
NOTE: Be sure to read this blog entry regarding an easy to use converter—Format Factory—that simplifies the process incredibly! It’s free (no cost) and works great!
1. Save the FLV video file to your desktop (Win/Mac/GNU_Linux doesn’t matter). We’re going to convert from FLV to MP4 and then from MP4 to MOV. I’m not sure why it has to happen that way, but to go directly from FLV to MOV generates errors for me.

2. Open VLC Media Player and go to FILE, then choose Streaming/Exporting Wizard.

3. When the Streaming/Transcoding Wizard window opens, choose to Transcode/Save to File then click NEXT.

4. Choose the FLV file you want to convert.

5. Skip the TRANSCODE window by clicking on NEXT. We’re just changing the “encapsulation” method.

6. Choose the correct encapsulation format (MP4 in this case)

7. Enter the name and location of the converted file.

8. Review the choices, then click FINISH to begin the process of encapsulation.

9. To convert from MP4 to MOV, just repeat the process above but at Step 6--where you choose the encapsulation format—choose MOV instead of MP4.
These works are licensed under a Creative Commons Attribution- Noncommercial- Share Alike 3.0 License.