Conventionally, people extract lignin from biomass using 1,4 dioxane. This lignin is regarded as the form in which at its closest to nature. However, the yield is very low, and therefore raises a concern over if this portion of lignin really is the representative of the whole lignin.

Fortunately, recent paper that introduces lignin extraction methods with high yield were just published

1. Gu, F., Wu, W., Wang, Z., Yokoyama, T., Jin, Y., Matsumoto, Y., 2015. Effect of complete dissolution in LiCl/DMSO on the isolation and characteristics of lignin from wheat straw internode. Industrial Crops and Products 74, 703–711. doi:10.1016/j.indcrop.2015.06.002

2. Capanema, E., Balakshin, M., Katahira, R., Chang, H., Jameel, H., 2014. How Well Do MWL and CEL Preparations Represent the Whole Hardwood Lignin? Journal of Wood Chemistry and Technology 35, 17–26. doi:10.1080/02773813.2014.892993

I personnaly tried it and the yield I got is 60-70%. 

Another way to get lignin, although not extraction, is to dissolve the other portion, cellulose and hemicellulose. The paper just came out 

3. Luterbacher, J.S., Azarpira, A., Motagamwala, A.H., Lu, F., Ralph, J., Dumesic, J.A., 2015. Lignin monomer production integrated into the γ-valerolactone sugar platform. Energy Environ. Sci. doi:10.1039/C5EE01322D

Hope this helps

There is no method that would not change the structure of lignin.

Every modification make changes.

The smallest changes are at MWL (milled wood lignin)

Is there any alternative of ball milling? Can I use Bead beating method (glass beads) for the same in sonicator instead of ball mill?

just have a check on definition of lignin: it can be  dissolved under specific conditions with specific solvents. lignin can be as different as conditions and solvents are. Depending on your scope you can define your own conditions, see whether the structure must be altered for a better dissolution or you want just the easily extractables, etc.

I do not know what the efficiency bead beating method but I think after a sufficiently long time, it might work. But much also depends on the overheating of the sample

Ball Milling is the crucial step in successful lignin extraction. As long as you can crush the biomass matrix, it will be okay.  I have no experience with bead beating and therefore cannot say for sure if it is strong enough. The paper I referred to in the first comment (the no.1) shows the picture of how the solution should look like if the biomass has been subjected to sufficient ball milling. If you use bead beating, you should continue doing so until you obtain the same clarity of solution. (If it appears cloudy, then it's not sufficient, you either have to do it longer or at higher frequency)

In term of heat generation, this is also an issue for ball-milling and hence you need to stop ball milling (or bead beating, if it creates heat, which it should, otherwise i'm sure it's not strong enough) once in a while to let the temperature cools down. In our lab we use liquid nitrogen to freeze the whole metallic container so that we ensure no heat damage to lignin.

Additionally, if you could turn off sonication it would be better. Sonication has been reported to induce minor structural change. Altho should not be a serious issue if you cannot. (Ref:  A. Yoshioka, T. Seino,M. Tabata and M. Takai,Holzforschung, 2000,

54, 357–364.)