Question about ultra sonic steeping?

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Venturing into DIY liquids. Going to buy an Ultra Sonic. Want to use a stoppered 250 ml Erlenmeyer Flask (I have 4 already) in USC machine but flask is 5.5" tall and well of machine is only 3" deep. I think that the water will cover the liquid at 200 ml (2.5" H). Does the well of the machine have to be covered or can I just use the machine without the well cover? Machine I'm looking at is an Isonic P4810 2L 30 min timer.
 
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