Fastest way to zero out low values in array?

from scipy.stats import threshold
thresholded = threshold(array, 0.5)

:)

This is a typical job for NumPy, which is very fast for these kinds of operations:

array_np = numpy.asarray(array)
low_values_flags = array_np < lowValY  # Where values are low
array_np[low_values_flags] = 0  # All low values set to 0

Now, if you only need the highCountX largest elements, you can even "forget" the small elements (instead of setting them to 0 and sorting them) and only sort the list of large elements:

array_np = numpy.asarray(array)
print numpy.sort(array_np[array_np >= lowValY])[-highCountX:]

Of course, sorting the whole array if you only need a few elements might not be optimal. Depending on your needs, you might want to consider the standard heapq module.