I'm going to start with this rough sawn piece of cherry. as you can see it has almost all the defects. Twist, cup, and bow. I don't have a powered jointer, but that's not a problem. The write up here is kind of long, but this process takes me on average 10 to 15 minutes for a board this bad. 

Here are the tools I'm going to be using for this task. A jack plane, a holdfast and notched batten (doe's foot) to keep things put on the bench, some shavings, and winding sticks    

First off, the easiest way to eliminate defects is to minimize them. This saves time, effort, and material. The board is about 6.5" wide. I only need a 3" wide board. I'm going to rip this before I do anything else.     

Before I rip it, I want to get the edge straight. I got lucky here, it's already pretty straight  

I'm using my jointer plane here. When I get a full length, full width, unbroken shaving, it's a good indicator my edge is pretty flat. I check to confirm

Because this board is rough still, and the faces are not yet parallel with each other I want to mark the face I used as a reference in case I need to reference it again    

Now I' m going to set my panel gauge to about 3 1/4" to strike a line and rip the board. My final thickness needs to be 3", but I will have 2 edges to joint so I want to give myself some breathing room. I strike a line on both faces and the edges with the panel gauge

I'm going to rip this with my 300mm Japanese rip kataba. This saw is extremely aggressive and makes quick work of this task. Starting the cut is really important. I want to make sure I start square

Before I get too deep, I check my line in the front

And check it from the back. I'm good on both faces, so it's time to rip

One "trick" with Japanese saws is to keep as many teeth engaged as you can. It's tempting to just saw horizontally and power through, but that will cause the thin blade to deflect and you will get a wandering cut. I saw at an angle

Now to flatten it. Before I start I have about 1" and a fat 16th to work with. This is 4/4 at the lumber mill I frequent. 

I'm going to use those shavings to shim the high parts of the board so it doesn't rock while I plane it. Otherwise I won't be removing the defects, I'll just be making a thinner defective board

These are winding sticks. they are moderately fancy. All your really need is two boards that are the exact same height and length. Many people use angle iron or even a 2x4. I have a contrasting strip at the top to make them more visible. I place them on the board with the contrasting strips facing eachother

Here is how they work. With the sticks at each end of the board. I crouch down and line up the edges. In a perfect world, the edges would be even with each other. You can see here that they are not

The arrows are pointing to where the board is high. Now if I plane from those two points, I will work out the defects

I highlighted in red the path I'm going to take with the plane. 

Now you can see where the red is missing. These were the high spots where the board had twisted. I take a few passes diagonally and check again

Now when I sight down the winding sticks, they are parallel with each other. The reveal between them is perfectly even. I've removed the twist    

.... Well sort of. I now move the winding sticks closer to each other and the center of the board and keep checking. There is more twist. I mark where the winding sticks are

The black pencil is my new planing path. I take a few passes like before and repeat the process

Then I clean off the bench. Of note, I keep my bench flat and check it often. If your bench isn't flat, do this against a known flat surface in your shop. I flip the board over so the side I was working on is against the bench. I then see if I can get the board to rock back and forth or side to side at all. If it lays flat and stays flat while I poke at it, I'm done

You can see there is still a lot of pencil left. This is because it's cupped. If you have a powered planer, this doesn't matter unless the board is really thin. I do have a powered planer so I'm going to send it through, this side down

I take light passes at first and make sure I'm not introducing more defects by checking for flat every few passes. Once this face is flat, I flip it over and fully flatten the face I took the twist out of earlier. Then I can take it to final dimensions 

After all that I only lost 1/16th of thickness. 

But because I flattened my reference face, the edge I jointed before is no longer square. I expected this to happen which is why I ripped the board wider than I needed to be initially

I jointed it the same way I did before and make sure it's flat and square

The final step is bringing the other edge in parallel on the tablesaw. Now I have an S4S board that is perfectly flat and square; and the edges and faces are perfectly parallel to each other. This will make joinery tasks much easier and save a lot of errors and mistakes going forward.