Intensity fluctuations at the output of a single mode fiber coupled to a He Ne laser I have coupled a Thorlabs HNL050L-EC - HeNe, 632.8 nm, 5 mW, Polarized Laser to a 2 meter long single mode fiber patch chord using a Thorlabs F230-FC-B aspheric lens. While I am certainly able to obtain a pure single mode Gaussian at the output, the total output intensity seems to be fluctuating over time scales of about a second. In some sense, the mode appears to be "breathing". The aspheric lens has been mounted on a stable mount, and the fiber is at the correct wavelength. I have also verified that the fluctuations are over and above the intrinsic fluctuations from the laser itself. Has anyone had this issue before? If so, what is the cause and what could be the best way to work around it to get a stable single mode Gaussian output?
P.S Please drop a comment if you require any further details to diagnose this issue. 
 A: My bet is that your fiber is very short (something like one meter or so) and that the fluctuations you see on the output mode are due to cladding modes, i.e. a part of the injected light propagating into the cladding of the fiber instead of the core. The resulting fluctuations are due to external perturbations of the fiber (thermal fluctuations or you touching the fiber and stuff).
Usually these modes are attenuated over long distances but I've already had this problem when using short fibers.
Try to shake your fiber or heat it up with your hands to see if it's doing something on the "breathing" that you see. If so then it could be those cladding modes. They should disappear when using a longer fiber though (for instance 5 meters).
A: This sounds as though the aberration in the laser's output could be fluctuating owing to "mode hopping" (where several of the laser's cavity modes are active and playing a time varying role) so that, even at a constant output power, the aberration of the output beam varies with time. Wavefront aberration is roughly the Fourier-dual of Strehl ratio. This quantity in turn is roughly the same as the coupling co-efficient of the wave into the single mode of a fiber, with equality holding if the fiber's mode field diameter and mode shape match the diameter of the Airy disk for the focussing lens.
In the past I have used the following effective technique to check for mode hopping ......... : couple the laser output into a single mode fiber, measure the laser's output power and watch for fiber output intensity fluctuations further to fluctuations in the power! In other words, I've used your exact setup!  So this isn't going to help you much because this is what you're seeing and you need some independent way to check that the phenomenon is what I am saying it is.
You could try focussing through a pinhole with the same diameter as that of the Airy disk for the focussing lens and check whether the "breathing" still happens. This would be a good sanity check, but it depends on experimental kit that is less mechanically stable than a fiber mounted on lens, so you'll need to be patient and quiet to check whether this setup gives the same results as your fiber. Otherwise, the pinhole output will vary even more wildly owing to mechanical vibration.
I would collimate the beam, or have it very slightly diverging, so that you can look at the farfield pattern on a wall (take due heed of laser safety considerations here); try imaging it through different polarizers so that mode hops may show up as farfield intensity variations. But this is not failsafe. 
The only sure fire way to detect mode hopping aside from with your setup is to input the laser into a point diffraction interferometer or other interferometer that makes its own reference (by passing one copy of the beam through a subresolvable pinhole to strip off any wavefront information and using this to build the interferogram). A wavefront sensor may achieve the same thing, but in my experience these will give you an accuracy of about 0.07 waves RMS. Much smaller aberration changes than this will lead to a well detectable difference to the coupling into a single mode fiber. 
A: Some other effects that might be at play:
1. Reflections from the end-faces of the fiber causing interference
2. Brillion Scattering
3. Check to see if in fact the fiber you're using has a cut-off wavelength shorter than the wavelength you're actually using.
A: Check the pointing stability of the laser, which, together with mechanical vibrations, would make the coupling efficiency fluctuate. After making the setup as mechanically stable as possible, try to put small diameter tubes everywhere around the beam before the fiber. And/or enclose everything in a box. Air movement has an effect, and it helps to block it. 
