Unfortunately, answering this is not easy, it depends on the details of your project. I found that complex projects often require specific configuration in the build script.
I'm going to assume that your projects have never been used in Eclipse. Here are some tips that may work for such cases (or they may not need more specific settings).
1) do not forget to apply the eclipse plugin to all your projects if they are simple Java projects or the eclipse-wtp plugin if they use war style web projects.
2) import your projects with disabled dependency management (this is one of the options in the import wizard.
If this does not work, I will need additional information about your projects and / or exactly what happens with the import. It looks like your projects do not have the proper Java character, or the source folders are not configured correctly. The contents of the .classpath and .project files for "poorly configured" projects would be helpful.
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