final IWorkspace workspace = ResourcesPlugin.getWorkspace();
Job cleanJob = new Job() {
  public IStatus run(IProgressMonitor monitor) {
    try {
       workspace.build(IncrementalProjectBuilder.CLEAN_BUILD, monitor);
       return Status.OK_STATUS;
    } catch(CoreException ex) {
      return ex.getStatus();
    }
  }
};
cleanJob.setRule(workspace);
cleanJob.schedule();