When you load Version 3.0 applications into a Version 5.5 image, warning messages such as "Defined global <name> in unmanaged namespace" might print to the System Transcript window. These messages indicate that you need to change your code so it runs cleanly on Version 5.5. The base migration tool can help you fix the code.
If you can load your applications, but they use any of the classes listed in Obsolete VisualAge code, load the configuration map VisualAge, Obsolete Parts, and then run the base migration tool.