I was used to have fruits normally after my main meal. Recently I read an article saying it is pointless and we need to try fruits on empty stomach or there should be an at least two hour gap with main meals to get the maximum amount of nutrition from fruits. If someone could explain the truth behind this that would be a great help.
This rumor is common enough that there is even a Snopes article about it.
In essence no, this doesn't help, and is in fact closer to the opposite of the truth. When eating a meal many more digestive enzymes and processes are started up then when only eating a small amount or say a pill. This is one of the reason you should always take your multivitamin with or immediately after a meal. The key factor here is known as gastric emptying, or how quickly the food is going through you. When it happens quickly, only the nutrients that are easy to absorb (like fats) are obtained. Eating more food at once (to a point) slows gastric emptying allowing for more complete digestion.
There are two key aspects when looking at the digestion of fruit. The first, and perhaps obvious, benefit is the absorption of nutrients. All of the calories, vitamins, etc that one can get out of fruit falls into this category. The second benefit is that of fiber which can help clear the gut of waste, bowel motility, maintenance of gut flora, and other uses that call for both soluble and non-soluble fibers which fruits are rich in. A very good review on their benefit can be found here.
But what about when they are mixed together with other things? When compared to milk and oatmeal, blue berries were found to have a synergistic effect with oatmeal, but milk was found to be inhibitory to both. If you are willing to take an example with pigs, fruits and vegetables protected against some of the more harmful effects of a high fat and protein diet when eaten at the same time (though this could be because of simple decreases in the fat intake).