Learning irregular words involves mental marking of irregular letters in the spelling, a process not fully understood. In a within-subjects experiment, we manipulated the type of scaffolding given to beginning readers to evoke mental marking. We pretested to sort 103 kindergarten and first-grade participants into sequential decoders, who decode letter by letter, and hierarchical decoders, who recognise vowel patterns. In the control phase, children read irregular words in sentence contexts with minimal scaffolding. In the experimental phase, participants read additional irregular words in sentence contexts by 'operating on the word' to mark irregular letters. Results indicated that the experimental condition induced better untimed word reading, but it did not improve spelling or reading in a flash presentation. Hierarchical decoders were significantly more successful than sequential decoders in untimed word reading, spelling and reading in the flash presentation. These results suggest that learning hierarchical decoding predisposes readers to learn irregular words.