Optimizing a python script with large arrays
You can get minor performance improvements if you use the += synthax of numpy, e.g. 

mainarr[0, lats, lons] = mainarr[0, lats, lons] + c550


would reduce to

mainarr[0, lats, lons] += c550


Though it is not really in-place, you still gain some speed.

Another idea I had, was to use numpy.clip as it might be faster than setting the upper bound for your indices manually. You may be able to gain further improvements using numpy.put with mode=clip instead of really clipping the values. Positive effects for numpy.take (which is the opposite of numpy.put) are described here.

I put up a little program to test the gain compared to your proposed code. As you did not provide much additional information, I had to do some assumptions, e.g. for the way your data looks like (see mock_data).

The result is something like the following

Experiment (10 files, 10000 points)
Original: 10.093s   Refactored: 9.964s

Experiment (10 files, 1000 points)
Original: 2.399s   Refactored: 2.362s

Experiment (10 files, 100 points)
Original: 0.349s   Refactored: 0.342s

Experiment (100 files, 10000 points)
Original: 47.823s   Refactored: 47.672s

Experiment (100 files, 1000 points)
Original: 10.888s   Refactored: 10.781s

Experiment (100 files, 100 points)
Original: 3.306s   Refactored: 3.195s

Experiment (1000 files, 10000 points)
Original: 423.727s   Refactored: 420.922s

Experiment (1000 files, 1000 points)
Original: 58.546s   Refactored: 56.579s

Experiment (1000 files, 100 points)
Original: 20.227s   Refactored: 18.260s


Conclusion

In my oppinion, you will not be able to gain a great speed-up by fiddling around with numpy here. I made a small test not included in the listing above with 1 file and 1M points

Experiment (1 files, 1000000 points)
Original: 51.245s   Refactored: 48.703s


Because of this I think numpy is not really the problem in your case. If your mask hits a lot of points, it might be a good idea to remove the corresponding indices from lats and lons with numpy.delete, because both lists will get shorter and mainarr[0][0] will not be messed up with all the values you put there.

As the operations on the files do not really depend on the other files, one could come up with the idea to split up the process and merge their results later. Your task would be to re-implement your function, so that you can run it in parallel in different processes for parts of your file list. But even this might not help you that much, if your I/O capacity is the bottleneck.

Test script

import numpy as np
import timeit

def mock_data(n_samples=1000):
    """Mock data generation"""
    lats = np.random.uniform(-90.0, 90.0, (n_samples, ))
    lons = np.random.uniform(-180.0, 180.0, (n_samples, ))
    c550 = np.random.rand(n_samples)
    c670 = np.random.rand(n_samples)
    c870 = np.random.rand(n_samples)
    cldy = np.random.rand(n_samples)

    return lats, lons, c550, c670, c870, cldy

def mock_files(n_files=500, n_data=1000):
    """Mock files for benchmarking"""
    np.random.seed(42)
    return [mock_data(n_data) for _ in range(n_files)]

def getmask(cldy, tresh, max_val, min_val):
    """Mock getmask"""
    return cldy &gt; (tresh / 2.0)


def original(files):
    """Original function by @Simon"""
    mainarr = np.zeros((4, 1800, 3600))
    i = 0

    #Loop over all input files
    for infile in files:
        lats, lons, c550, c670, c870, cldy = infile

        lats = np.array(np.round((lats+90)*10), dtype=np.int16)
        lons = np.array(np.round((lons+180)*10), dtype=np.int16)

        lats[(lats&gt;=1800).nonzero()]=1799
        lons[(lons&gt;=3600).nonzero()]=3599

        #The function below is already optimized
        masker = getmask(cldy, 1.0, 1.0, 0.0)
        pts = (masker != 1).nonzero()
        lats[pts] = 0
        lons[pts] = 0

        mainarr[0, lats, lons] = mainarr[0, lats, lons]+c550
        mainarr[1, lats, lons] = mainarr[1, lats, lons]+c670
        mainarr[2, lats, lons] = mainarr[2, lats, lons]+c870
        mainarr[3, lats, lons] = mainarr[3, lats, lons]+1

        i = i+1

    return mainarr


def refactored(files):
    """refactored function by @Alex Vorndran"""
    mainarr = np.zeros((4, 1800, 3600))

    #Loop over all input files
    for i, infile in enumerate(files):    
        lats, lons, c550, c670, c870, cldy = infile

        lats = np.array(np.round((lats+90)*10), dtype=np.int16)
        lons = np.array(np.round((lons+180)*10), dtype=np.int16)

        np.clip(lats, 0, 1799, out=lats)
        np.clip(lons, 0, 3599, out=lons)

        #The function below is already optimized
        masker = getmask(cldy, 1.0, 1.0, 0.0)
        pts = (masker != 1).nonzero()
        lats[pts] = 0
        lons[pts] = 0

        # make use of "in-place" additions
        mainarr[0, lats, lons] += c550
        mainarr[1, lats, lons] += c670
        mainarr[2, lats, lons] += c870
        mainarr[3, lats, lons] += 1.0

    return mainarr


def validate_refactoring(n_files, n_data):
    """Validate the refactoring with comparison by value"""
    files = mock_files(n_files, n_data)
    mainarr_o = original(files)
    mainarr_r = refactored(files)
    return np.allclose(mainarr_o, mainarr_r)


def test_functions():
    """Test different versions"""
    n_runs = 100
    n_files_all = (10, 100, 1000)
    n_data_all = (100, 1000, 10000)

    # a list of tuples where the first element is the number of files
    # and the second one is the number of elements
    files_and_points = [(  10, 10000), (  10, 1000), (  10, 100),
                        ( 100, 10000), ( 100, 1000), ( 100, 100),
                        (1000, 10000), (1000, 1000), (1000, 100)]

    assert validate_refactoring(10, 100)

    imports = 'from __main__ import original, refactored, mock_files;'

    for n_files, n_data in files_and_points:
        data = 'files = mock_files({}, {});'.format(n_files, n_data)

        time_original = timeit.timeit(
            'original(files)', setup=imports+data, number=n_runs)
        time_refactored = timeit.timeit(
            'refactored(files)', setup=imports+data, number=n_runs)

        print('Experiment ({} files, {} points)'.format(n_files, n_data))
        print('Original: {:.3f}s   Refactored: {:.3f}s\n'.format(
            time_original, time_refactored))

if __name__ == '__main__':
    test_functions()