@Teginder, you asked "But I think, it is really tough to understand what type of a link is organic ? Sometime I feel a links seems pretty natural is also gets caught under Google violation radar. WHY?"
The likely answer is your thoughts about whether a link is organic or manipulative are not calibrated to how Google views links. It takes a lot of time and experience to consistently reach the proper diagnosis for each link.
@Monali, you asked about links from "your sister websites". In my experience, people who ask this type of question have many "sister websites" and the links are likely deemed to be manipulative. Why offer the link from "500 pages"? Is the link relevant for users on all those pages?
You need to be VERY careful when you create a link from one of your owned websites to another, especially if you have been already caught violating Google's Quality Guidelines. The safest approach is to either remove, nofollow or 302 the links from your own websites which point at each other.
If you operate two websites where website A sells sneakers and website B sells socks, then it may make sense to provide links from the sneaker site to the sock site on most pages. With that said, it would likely be best to simply combine the websites into a single site.
The summary here: it is possible for a site owner to provide links between two sites which are not manipulative, but the links need to be presented in a high quality manner. The overwhelming majority of site owners who ask me this type of question operate many websites, have a manipulative link issue, and the interlinking between their own websites is a contributing factor to that issue.