Importing of big files:right approach?
There are two algorithmic aspects to your code which concern me. The most significant problem is that you read the entire file in to memory before you start processing the data:

filelist = a.readlines()


This is an inefficient way to do things with large input files.

You should instead be reading the data 1 line at a time and processing each line as you get it. This allows you to have a much smaller memory 'footprint', and it allows you to discard data that you do not need.... instead of your while loop while count &lt; leng consider the approach:

for line in a:
    ....


This should reduce your memory significantly.

(Asker updated question....)

The second issue you should consider changing is using numpy arrays for the vectorr method as well. This array is about the same size as the final array and you are incrementally allocating memory for it. Doing it with a single initializer (perhaps vect = empty((I*J*K, 3)) ) would be worth considering.