One of my favorite activities is to photocopy a story or part of a book that my class is reading and have them take highlighters or colored pens and find all of the words that they think have a prefix or suffix. Thenn we copy them onto idex cards or paper slips. You tell them which words actually have affixes and which do not. Finally, kids sort the cards into words with the same prefix or suffix, and then try to guess what the word means and what the prefix or suffix means. Making it a game means they will remember the meaning better when you do tell them. What makes this activity good for SPED is that it reinforces the bigger idea of what is and is not a prefix or suffix.
Perhaps you can set up short dialogues in which the students see/hear how the absence or addition of an affix to a word changes the meaning. The creation of characters who speak in these dialogues might also amuse students:
A character such as Mrs. Re- whose repeats and returns to ideas....
The Trans-Man who keeps going across the room
Let the students role play and give them a dialogue in which they add their assigned affix. The sillier the better, for people remember what they have laughed about, do they not?
I have a flip book that has prefix, root, suffix combinations and we look at which combinations make real words. Repeated use of this patterning helps to establish that these are components which make words, but that not all combinations work.
I think I would start with easy words that students can identify. Perhaps have a colorful picture with the word beneath.
See if the kids can organize the words based on similar meanings, esp. with regard to words that share the same roots, prefixes or suffixes. I would probably do them separately.
Things like -ject, micro-, or tri- might be great starting points. For example, tricycle would be a familiar word. Tripod has the tri-, as well as triple. I think that pictures and colors are naturally engaging, even if they do the coloring themselves. The more like a game it is, the better.
Working with this material is great for helping kids figure out the meaning of unknown words that are similar to works they already know, and I think all kids should learn this, not only for the classroom, but for PSAT and SAT testing.
If you provide students with prefixes, suffixes and/or root words, you could have students use a dictionary or an online etymology site and find words that have that root in them. They could then write a definition so that they can see the root "in action" in a word they might actually use. If they can see the connection that all words that start with "de" have something to do with being "away" or "apart from" then they have a word attack skill for unknown vocabulary.
The more areas of processing you can incorporate the easier it will be for students to retrieve the learned information. Connect the learning and reviewing to music, movement, sight, and etc. You might have them search through local newspaper articles to find examples of the prefixes and suffixes. The more real world usage, the more students will be willing to learn.
Not sure what age you are talking about, but with most special education students you will need a way to relate their learning to something familiar to them. Also lots of repetition is required. I might try flash cards with the prefixes and suffixes, you might even consider putting them on a word wall. I have also seen a teacher play Bingo with suffixes and prefixes.