Yes, this is possible:
C#:
Imap imap = new Imap();
...
imap.SetMessageFlags(id, ImapFlagAction.Replace, ImapMessageFlags.Flagged | ImapMessageFlags.Answered | ImapMessageFlags.Seen);
VB.NET:
Dim imap as New Imap
...
imap.SetMessageFlags(id, ImapFlagAction.Replace, ImapMessageFlags.Flagged Or ImapMessageFlags.Answered Or ImapMessageFlags.Seen)
This will set "Flagged", "Answered" and "Seen" flags on the specified message and remove any other flags.