If the funds are up 100% you'll only owe 7.5% federal tax on the amount withdrawn assuming you are in the 15% cap gains bracket.
That's very favorable tax treatment compared to to other sources of income withdrawn from other sorts of accounts.
You could have avoided paying 7.5% tax by keeping the money safe in a bank earning nothing for the past 4 years and have 50% less.
In retrospect not a winning strategy.
Obviously if you want to minimize tax paid now, sell the funds and shares that have the lowest gains.