is there a way to remove the table out of rendered html that is created by the h:selectManyCheckbox tag in server faces?
I am using twitter bootstrap an
You could just render a bunch of <h:outputLabel><h:selectBooleanCheckbox> inside <ui:repeat>. This way you've markup freedom. You'll only need to alter the model from e.g. List<T> to Map<T, Boolean> to represent the checked values and then loop over the map afterwards to collect checked ones.
A ready-to-use component is Tomahawk's <t:selectManyCheckbox> which has an additional layout attribute value of spread.