With the prominence of annoying tanks such as Alistar and Amumu, as well as annoying tanky DPS such as Jarvan IV, Irelia, Warwick, Udyr, etc., this build is designed to win a solo lane (preferably top where you can afk farm easier) and make these tanks useless later in the game. It does this by exploiting Miss Fortune's naturally high damage output of both phsyical and magic types, and maximizes these against tanks by using runes and items to penetrate their defenses. Even though you may not have an optimal damage output with this build, you should be so far ahead that your damage is strong anyway, and is always as close to true damage as possible.

For runes, I run magic penetration quints and blues, armor penetration reds, and flat mana regen yellows. The mana regen helps you use E frequently to harass and zone during the laning phase, and the remaining runes ensure that you have strong penetration from both your physical and magic damage sources early on, even before you complete key components of your item build.

In a solo lane, you do not need the experience mastery in utility if your ult does not provide CC to dominate the lane. For instance, I WOULD take the experience mastery as Warwick because his ult lets you get a kill if you had any semblance of decent harass pre-6. But with MF, people can just sidestep her ult, and it doesn't add to your lane dominance that much. Therefore, 21 points in offense maximizes damage output, and 9 in defense allows you to trade hits better with stronger armor and magic resist, and regenerate your health quicker.

Since I choose to max E first, I focus first on magic pen before armor pen. I open with an amplifying tome and a pot. While others may start boots in a solo lane, MF's passive strut gives her movespeed to last hit and get in and out quickly. I typically grab boots1 before finishing Haunting Guise, and soon after I get Sorc Boots and Ghostblade to ensure that my movespeed remains dominant even as enemy champions buy their respective movespeed items. At this point, many enemy champions may not have that much armor or MR, so your attacks and skills do very strong damage. As they build armor/MR, you counter with Void Staff for mpen and Last Whisper for arpen. The order of Void/LW in the build is dependent on the enemy's build - either your lane opponent if the laning phase is long, or the tanks/tanky DPS if there are many teamfights and skirmishes early.

Finally, your luxury item is Madred's Bloodrazor, which does percent health damage, and your high magic penetration ensures that this number is as close to true damage as possible. If played right, you will finish your build ahead of your opponents, and will melt them regardless of how they try to defend against you. Alternatively, the last item can be Phage into either Trinity Force (for strongest damage all around, Sheen procs, etc. etc.) or Frozen Mallet (for guaranteed slow on autoattacks). I get Trinity Force if the team only has one tank, and Frozen Mallet if I am so far ahead that I am only concerned with chasing down stragglers after fights. I would say I go 70% Bloodrazor, 20% Mallet, and 10% Triforce, but it all depends on context.

Getting E with high magic penetration is a strong harass, and keeps melee champions from farming against you. Therefore I get E first and max it first (besides ult at 6/11/16, of course). I max W second because the anti-heal component counters sustainable top laners (which are obscenely common nowadays), and the attack speed can help if you push and poke towers. I get one point in Q at level 4, because it is a viable harass, but max it last. Typically ult is difficult to land in teamfights and the long channel makes you vulnerable, so unless you have a teammate with AoE CC (think Amumu, Kennen, etc.), just use ult to push minion waves when appropriate.

I opt for Flash/Ignite as my summoners. Flash is the most OP thing in the game and absolutely mandatory for everyone, and Ignite is another anti-heal to complement your Impure Shots, plus with the Ignite mastery, you gain more AP when Ignite is on CD as an added bonus. Also, Ignite can help you push an early kill in lane if your harass is strong enough.

While Flash is mandatory, Exhaust, Ghost, or Clarity can substitute for Ignite based on user preference. I have had the most success with Ignite, but if you choose not to run it, make sure to update your masteries so that point doesn't go to waste!

You should be able to last hit with auto-attacks, but if against a melee laner who is also trying to last hit, you can punish with autos and E, which will probably land a few CS and push your lane. Pushing can be good, but make sure your lane is warded so you can escape gank attempts. Also, be much more careful about pushing when your Flash is on CD, as you no longer have your "OP Get out of Jail Free Card." Seriously, Flash is ridiculous.

In teamfights, since you can melt any target, you want to remain as safe as possible in the back of teamfights. Don't worry about "high priority" enemy targets; just make sure you aren't in range of them. If you are hitting their tanks and vice versa, you will win the fight by doing stronger damage and forcing their squishies to retreat when there's no one left to bodyguard them.

Beat up tanks and tanky dps, glhf! :-D