This is the script I use to convert FLAC files to MP3. After converting, it moves all the FLAC files into a subdirectory named .flac:
#!/bin/bash
#------------------------------------------------------------------------------
# Converts all FLAC files in the current folder to high-quality VBR MP3s.
# Moves all .flac files into a folder named .flac.
#------------------------------------------------------------------------------
for f in *.flac; do  
    ffmpeg -i "$f" -qscale:a 0 "${f[@]/%flac/mp3}"
done
mkdir .flac
mv *.flac .flac/
echo Done.
This script requires ffmpeg. Install using:
sudo apt-get install ffmpeg