I was looking at the doctor doom from the fantastic 4 starter set, and I saw that his special power "armored mastermind" gives him invulnerability and mastermind. I was wondering if those powers can be used on the sane attack. Like if I take 3 damage can I reduce it by two and then mastermind the rest?

No. Master Mind transfers Damage dealt. Invulnerability reducers Damage dealt. Once you choose to reduce it, you can't then transfer it.

Invulnerability
(Non-Optional) Damage dealt to this character is reduced by 2.

Mastermind
When this character would be dealt damage, you may instead choose to have all the damage be dealt to a single adjacent friendly character with a point value less than this
character’s. Any additional effects of the damage dealt (knock back, penetrating damage, etc.) are applied to the character taking the damage. Damage dealt by this power is not an attack.

Ohhhhhh okay. I was thinking invulnerability reduced damage dealt and then mastermind would let you transfer that damage dealt to someone else. But I see what you mean and that makes more sense. Thanks!

So lets say Dr Doom is attacked and the result of the attack is 5 clicks of damage coming his way.

What is the chain of events now?

I would interpret this as:

A) 5 clicks of incoming damage to Dr Doom is reduced to 3 because of the invulnerability power. (again this is a non-optional step as the ability states).

B) Dr Doom can then mastermind the 3 damage he would take to any adjacent character who is worth less points then him as the ability states.

Based on the way the rules are written I don't see why I can't utilize both abilities for this effect. I didn't chose to reduce the damage, as the invul ability is non-optional, and Dr Doom would be dealt damage still allowing the use of the mastermind ability.

Apologies if there is a basic concept or principle I am missing here, I am very new to heroclix (although I did just win my first 4 person free for all last night!).

In this case, again I see nothing to imply that these abilities can't be combo'd together. Not allowing both abilities to be used together makes the entire special skill pointless. The way you are describing it working means I would never be able to use the 'mastermind part' of this special ability which doesn't make any sense. Also, note that the special skill description reads AND.

ARMORED MASTERMIND: Dr. Doom can use Invulnerability and Mastermind.

If someone can please clarfiy this situation for me that would be great, because its just one of many questions that I have, that come up.

Due to the wording of Mastermind, you need to use it before the character would actually be dealt any damage. So you can either transfer damage with Mastermind OR you can deal the damage to the MM character and use any damage reducing powers it may have.

It's a sequence of events thing. Mastermind activates when a figure would be dealt damage, damage reducing powers do not activate until after damage is dealt, so Mastermind goes first. One or the other.
And just so you know you do not have to use either power if you don't want to.

Also, note that the word "and" between powers does not necessarily mean they can be used together. Justice League Flash has a power called Vibration.

From the Player's Guide:
That does not mean he can use them together. Hypersonic Speed requires a power action to activate. Phasing/Teleport requires a power action to activate. Flash can only be given one non-free action per turn. And that non-free action can only activate one effect. So Flash could use Hypersonic Speed or he could use Phasing/Teleport. He cannot use them both together.

Ok, so I believe this answers one of my questions but raises another.

Using the same example your saying that:

Dr Doom is the target of a successful attack which would deal him 5 clicks of damage. At this point, I would have to activate my mastermind ability, if I wanted to use it at all.

If I chose not use MM, then I am dealt 5 clicks of damage, which is then reduced to 3 clicks by the invul ability.

That seems straightforward.

Here's my next question:

And just so you know you do not have to use either power if you don't want to. .

Isn't the invul ability (specifically stating that the ability is non-optional) specifying that I must apply its damage reduction whether I want to or not?

I believe that the reasoning is that Dr. Doom doesn't actually possess the Invulnerability power, he can only use it, what he actually has is Armored Mastermind.

Since SP are optional (unless otherwise stated) he doesn't have to use Invulnerability. Someone correct me if I am wrong.

correct it says that he may use Invul, does not say that he must use it.

You're not wrong.

I see now, that makes much more sense why they would have written the special ability as such. Thanks for the explanation.