This is the most time-consuming aspect of collecting and saving seeds. But it is a necessary part of the process.
The simplest and most common way to separate dry seeds from the plant parts holding them is to pinch the dried pieces between your fingers until the seeds fall out. Besides allowing them to mature, permitting the seeds to dry out before collecting them makes this effort easier.
In the vegetable garden, big seeds tend to be the quickest to collect. Crush a pod of peas or beans and the dried, hard seeds inside separate easily from the thin exterior shell. These kind of seeds are sturdy and you can grab a bunch and roll them in your hands until the dried pods are pulverized, leaving behind the seeds.
The same procedure works for smaller dry seeds too. A pinch of the fingers separates the seeds from the plant pieces. Usually the color of the seed is different from the rest of the plant so you can tell which is which.
It's the opposite for most small seeds. I collect the seeds on the sheet of paper, remove the larger pods or plant pieces, and pour the seeds into the clean container.
You can put a large amount of pods, stems, or dried flowers in a bowl or bucket and crush the mass to shred it. When the protective shells break apart, the dried seeds will fall to the bottom for collecting. You can also put the seeds and plant pieces in a paper or cloth bag and roll it around to crush what's inside.
To me, this tends to create a big mess and it takes just as much time to separate the seeds from the pulverized plant pieces because so much of the pile is waste material. Also, regardless of how much you pound it, there are always some of the seeds clinging to pods and stems and you still need to comb through the mass to separate and collect all of the seeds.
You can try a few methods to separate the chaff from the seeds if you choose to do a mass crushing method.
I find there are always stem pieces that are the same size as or smaller than the seeds so a secondary separation is still required. Putting the mixture on a sheet of paper and picking out the seeds from chaff still works well. Tweezers may be necessary when fingers are too bulky.
For some seeds that are definitely heavier than the pulverized chaff, a little breeze can help. While leaving them in the bowl or while slowly pouring them out, gently blow across the surface so that the chaff is blown away and the seeds fall to a collecting mat. If you're mechanically inclined, a small fan set on low may achieve the same effect. Depending on the strength of the air, the chaff can be blown around quite a bit and create a widely-distributed mess.
For small seeds, a screen, colander, or sieve can be beneficial. When you place the chaff and seed inside and crush it all, the small seeds will drop through the holes leaving larger pieces behind. This is an efficient way to separate the big pieces, but you still have small chaff mixed with the small seeds.
For most wet seeds, the process is easy and straight-forward. Scoop the seeds out of the fruit and separate them from the pulp. Many wet seeds are large so they're easy to work with. Washing the seeds and pulp in a bowl of water works well to separate the seeds with your fingers.
Squash and pumpkin seeds are a breeze. Pull them from the flesh of the fruit and place the seeds on a paper towel or sheet of newspaper to dry. You want all of your seeds to be dry before storing so you don't have rot or mold problems.
Other wet seeds that are encased in a very wet, fleshy pulp, like tomatoes and cucumbers, need to be fermented before drying the seeds. This helps break some of the protective covering and encourages better germination later on. For these types of fruits, place the seed and pulp in a bowl and leave them alone for three to five days. They'll ferment and a mold will develop on top. At that point scoop as much of the mold and pulp off as you can, then add water and mix it all up.
Don't try to accelerate the drying time by putting seeds in the oven or near a heat source. Just let them air dry naturally. Larger seeds will take longer than smaller ones. In a week or two the seeds will be dry. Have patience.
When the seeds you've collected are dry, they're ready for storage. Choose a clean, dry container as your storage vessel. Many gardeners use paper envelopes. They're easy to write on which makes it easy to identify the type of seed and the date you saved it, both important things to know when you're ready to sow later on.
I like to use small, glass jars and bottles. I label them with a strip of masking tape. It's a good way to recycle household items. I also think jars do a better job of maintaining a dry environment; exposure to liquids will soak an envelope and the seeds inside. Seeds are alive and need some exposure to air, but the amount in a jar should be enough.
Most seeds can remain viable for three to five years after collecting, though they'll do best the sooner they're used. Proper storage conditions, like in a refrigerator, extends the storage time. It's best to keep seeds from different years separated in storage. That's another reason to label them. You'll know which ones are oldest and can choose to sow those first or discard them if the viability is in question.
Allowing plants to produce seeds and then collecting them is totally natural and easy to do. By adding this task to your annual gardening list you can establish a seed bank of your own and enable yourself to sow next year's garden from this year's or last year's crop. This makes your garden self-sustaining and will save you big bucks over time. I like those options.
Check out my previous articles for more information on the entire process for saving seeds.