I used to run a website, and ads on the site were the source of income from the site. I used to disguise the ads in the contents of my site so people would click on the ads thinking they were contents of the site. The method was strictly prohibited by the ads provider company. I made a handsome amount out of this technique. We used to pay money to get traffic on the website. So it was about we pay 1$ and earn around 5$ out of it. We then built a house in which around 65% amount was paid by me from that money and other 35% was paid by my father's money. We now are living in that house. This house that we built, was built without any approval of the map from the Govt, and when govt. officials came on inspection we used our contacts to keep them silent. Now that ALLAH (s.w.t) has granted me Hidaya (Al-Hamdo LILLAH), I have left all that and now am stick to my job and halal earnings only. I am moving out of country now. The question arises what do we do with this house now? As it is not only illegal construction but haram money is also used on it, are we bound to sell it away and not benefit from it? If yes then what do we do with that money after selling it? Should that money go to charity? all of it or I can keep what I spent to get traffic on my site and only pay my profit to charity? Or if my father doesn't allow me to give it to charity (as they would be in a dire need of buying another house for them) is it okay to leave all my rights on that money to my father and have no claim of mine on it even when it comes in inheritance, as I have heard spending on parents is also a form of charity?

All perfect praise be to Allaah, the Lord of the Worlds. I testify that there is none worthy of worship except Allaah, and that Muhammad, sallallaahu ‘alayhi wa sallam, is His Slave and Messenger.

It appears from your question that what you had been doing is clear cheating and contravening the conditions of the company in deserving the fees from the advertisements; therefore, in order to be acquitted from sin from this money that was taken without right, you must do either of the following:

1- You have to seek the forgiveness of the owners of this company, and if they absolve you of their rights, then you are not required to do anything else. 

2- If they do not absolve you, then you are obliged to give the money back to them, and if you do not know exactly its amount, then you should endeavor to estimate it according to what you predominantly think would acquit you from sin, but it is not sufficient that you give it in charity while you are able to give it back to its rightful owner.

As for your traffic in the site and your earnings from it, if it is lawful trade, then you deserve the profit. If you obtained the capital money in that manner as well as the house that was built from this money and with other money, then you are not obliged to get rid of it, rather you may dispose of it as you wish, by selling it, renting it or dwelling in it. This is because the money of the company which you had taken without right is a debt which you are personally liable to repay, but other matters are not related to this [i.e. the sin of taking that money is related to you and not to the money itself. For more benefit, please refer to Fatwa 130992.

Concerning what you mentioned in regard to contravening the law and using your contacts (to keep the government officials silent), then you are only required to seek the forgiveness of Allaah and this is the expiation for such actions. This has nothing to do with the lawfulness of the house and the permissibility of disposing of it as you please.

Allaah Knows best.