I removed the two agents (AD and FIM Syn) and their ConnectorSpace, in the metaverse and the portal linked objects remained. when I delete this objects in portal - they are re-sync and recreate in portal and in AD... how to completely clean the metaverse?

Check your Object Deletion Rule in the Metaverse Designer.http://www.wapshere.com/missmiis

can I manual delete old objects? in SQL tables? I recreate MA with same names and Configure Object Deletion Rule does not show old objects...

No no no, you can't do that. Orphans in the metaverse can be a problem. The only way to delete them is to get them joined back to something first, then you can delete them in the provisioning code. The reason you have to join them to a connector space object first is this: the sync service starts the sync cycle with objects found in the connector space you are syncing. There is no way to "sync the metaverse" independantly of connector space objects. Depending where you are it may just be easier to start over with a new FIMSynchronizationService database. First you can export your metaverse schema and your MA configurations so they will be easy to re-import in the fresh database. The way you start with a new database is by reinstalling the sync service. If you don't want to do that then, as I said above, you need to get those orphans joined to some kind of connector space object. Which means they need an attribute on them that can be used in a join rule. Do the orphans have any attributes left on them or were they all recalled? And for the future - get your deletion rule correct. The usual way is to delete the metaverse object when the last CS object has been disconnected.http://www.wapshere.com/missmiis

Can I programmatically using managed code or powershell, change the object in the metaverse?

the only right way to delete objects in MV is to set up object deletion rule. if you want total cleanup in MV - turn off sync rules provisioning and turn off MV provisioning extension rules then change object deletion rule to 'when any of the following MA is disconnected' and select proper MAs. then either delete MA connector space or manually disconnect CS objects from MV entry. once done - turn provisioning on.