The problem is that the folder directory is /home/marek/Desktop/Tekkitserver/3.1.1 and root has all but 5 file ownership and permissions what are inside it.
It all happened after I launched tekkit server .bat file trough terminal and when I opened folder with "home folder" I saw that freshly created files are in total root access.
And none of the sudo nautilus commands worked, because the folder was unreachable for nautilus.
I was able to see no child folder even whit Ctrl+H and I have troubles with chown. My user name is Marek Parbo (marek) and I am an administrator.
And I know that this question is recently asked, but i really didn't understood it at all. I have experience with sudo nautilus because Root was so defensive that and freshly formatted SD card was only permissioned to root and i got rid of it whit sudo nautilus.
However, this time i can't use it.

chownand how exactly doessudo nautilus(which is discouraged for many reasons, btw - usegksu nautilusif you really need a rootnautilusinstance) not work? – FEichinger Jan 2 at 17:39