Ignore package in update manager
Then you need to do an apt-pinning, to prevent future updates:
Create a new file in /etc/apt/preferences.d/ (if Ubuntu >= 10.4) named after your program, with following entry:
Package: program
Pin: version 1.2.3*
Pin-Priority: 1000
assuming, you know that your programs version, you want to freeze, is 1.2.3
1 - Go to Synaptic Package Manager
2 - Enter [package name] into the search field
3 - Highlight the installed package
4 - Click on Package on the top row
5 - Select Lock Version
Done, now [package name] will no longer be updated.