Running as root are we? Not recommended.
It seems that you are using the Brother scan -key tool. The destination for the files is set in /opt/brother/scanner/brscan-skey/script/scantofile-0.2.4-0.sh on my system.
You could change the path highlighted in blue.
The alternative is to use a scanning program e.g.xsane, skanlite and capture images in the format and resolution you want to a path you choose.